1
|
van den Driest L, Kelly P, Marshall A, Johnson CH, Lasky-Su J, Lannigan A, Rattray Z, Rattray NJ. A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer. Comput Struct Biotechnol J 2024; 23:2200-2210. [PMID: 38817965 PMCID: PMC11137368 DOI: 10.1016/j.csbj.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
Breast cancer is a multifaceted disease and a leading cause of cancer morbidity and mortality in females across the globe. In 2020 alone, 2.3 million women were diagnosed and 685,000 died of breast cancer worldwide. With the number of diagnoses projected to increase to 3 million per year by 2040 it is essential that new methods of detection and disease stratification are sought to decrease this global cancer burden. Although significant improvements have been made in breast cancer diagnosis and treatment, the prognosis of breast cancer remains poor in some patient groups (i.e. triple negative breast cancer), necessitating research into better patient stratification, diagnosis and drug discovery. The UK Biobank, a comprehensive biomedical and epidemiological database with a wide variety of multiomics data (genomics, proteomics, metabolomics) offers huge potential to uncover groundbreaking discoveries in breast cancer research leading to improved patient stratification. Combining genomic, proteomic, and metabolic profiles of breast cancer in combination with histological classification, can aid treatment decisions through accurate diagnosis and prognosis prediction of tumor behaviour. Here, we systematically reviewed PubMed publications reporting the analysis of UK Biobank data in breast cancer research. Our analysis of UK Biobank studies in the past five years identified 125 publications, of which 76 focussed on genomic data analysis. Interestingly, only two studies reported the analysis of metabolomics and proteomics data, with none performing multiomics analysis of breast cancer. A meta-analysis of the 76 publications identified 2870 genetic variants associated with breast cancer across 445 genes. Subtype analysis revealed differential genetic alteration in 13 of the 445 genes and the identification of 59 well-established breast cancer genes. in differential pathways. Pathway interaction analyses illuminated their involvement in general cancer biomolecular pathways (e.g. DNA damage repair, Gene expression). While our meta-analysis only measured genetic differences in breast cancer due to current usage of UK Biobank data, minimal multi-omics analyses have been performed and the potential for harnessing multi-omics strategies within the UK Biobank cohort holds promise for unravelling the biological signatures of distinct breast cancer subtypes further in the future.
Collapse
Affiliation(s)
- Lisa van den Driest
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Patricia Kelly
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Alan Marshall
- School of Social and Political Science, University of Edinburgh, Chrystal Macmillan Building, George Square, Edinburgh EH8 9LD, UK
| | - Caroline H. Johnson
- Yale School of Public Health, Yale University, 60 College Street, New Haven, CT 06510, USA
| | - Jessica Lasky-Su
- Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Ave, Boston, MA 02115, USA
| | - Alison Lannigan
- NHS Lanarkshire, Lanarkshire, Scotland, UK
- Wishaw General Hospital, NHS Lanarkshire, 50 Netherton St, Wishaw ML2 0DP, UK
| | - Zahra Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
- NHS Lanarkshire, Lanarkshire, Scotland, UK
| | - Nicholas J.W. Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
- NHS Lanarkshire, Lanarkshire, Scotland, UK
| |
Collapse
|
2
|
Wang Y, Zuo J, Duan C, Peng H, Huang J, Zhao L, Zhang L, Dong Z. Large language models assisted multi-effect variants mining on cerebral cavernous malformation familial whole genome sequencing. Comput Struct Biotechnol J 2024; 23:843-858. [PMID: 38352937 PMCID: PMC10861960 DOI: 10.1016/j.csbj.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/04/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Cerebral cavernous malformation (CCM) is a polygenic disease with intricate genetic interactions contributing to quantitative pathogenesis across multiple factors. The principal pathogenic genes of CCM, specifically KRIT1, CCM2, and PDCD10, have been reported, accompanied by a growing wealth of genetic data related to mutations. Furthermore, numerous other molecules associated with CCM have been unearthed. However, tackling such massive volumes of unstructured data remains challenging until the advent of advanced large language models. In this study, we developed an automated analytical pipeline specialized in single nucleotide variants (SNVs) related biomedical text analysis called BRLM. To facilitate this, BioBERT was employed to vectorize the rich information of SNVs, while a deep residue network was used to discriminate the classes of the SNVs. BRLM was initially constructed on mutations from 12 different types of TCGA cancers, achieving an accuracy exceeding 99%. It was further examined for CCM mutations in familial sequencing data analysis, highlighting an upstream master regulator gene fibroblast growth factor 1 (FGF1). With multi-omics characterization and validation in biological function, FGF1 demonstrated to play a significant role in the development of CCMs, which proved the effectiveness of our model. The BRLM web server is available at http://1.117.230.196.
Collapse
Affiliation(s)
- Yiqi Wang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Jinmei Zuo
- Physical Examination Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Chao Duan
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Hao Peng
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Jia Huang
- The Second Clinical Medical College, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730030, Gansu, China
| | - Liang Zhao
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Li Zhang
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Zhiqiang Dong
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| |
Collapse
|
3
|
Bhattacharyya N, Chai N, Hafford-Tear NJ, Sadan AN, Szabo A, Zarouchlioti C, Jedlickova J, Leung SK, Liao T, Dudakova L, Skalicka P, Parekh M, Moghul I, Jeffries AR, Cheetham ME, Muthusamy K, Hardcastle AJ, Pontikos N, Liskova P, Tuft SJ, Davidson AE. Deciphering novel TCF4-driven mechanisms underlying a common triplet repeat expansion-mediated disease. PLoS Genet 2024; 20:e1011230. [PMID: 38713708 PMCID: PMC11101122 DOI: 10.1371/journal.pgen.1011230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/17/2024] [Accepted: 03/19/2024] [Indexed: 05/09/2024] Open
Abstract
Fuchs endothelial corneal dystrophy (FECD) is an age-related cause of vision loss, and the most common repeat expansion-mediated disease in humans characterised to date. Up to 80% of European FECD cases have been attributed to expansion of a non-coding CTG repeat element (termed CTG18.1) located within the ubiquitously expressed transcription factor encoding gene, TCF4. The non-coding nature of the repeat and the transcriptomic complexity of TCF4 have made it extremely challenging to experimentally decipher the molecular mechanisms underlying this disease. Here we comprehensively describe CTG18.1 expansion-driven molecular components of disease within primary patient-derived corneal endothelial cells (CECs), generated from a large cohort of individuals with CTG18.1-expanded (Exp+) and CTG 18.1-independent (Exp-) FECD. We employ long-read, short-read, and spatial transcriptomic techniques to interrogate expansion-specific transcriptomic biomarkers. Interrogation of long-read sequencing and alternative splicing analysis of short-read transcriptomic data together reveals the global extent of altered splicing occurring within Exp+ FECD, and unique transcripts associated with CTG18.1-expansions. Similarly, differential gene expression analysis highlights the total transcriptomic consequences of Exp+ FECD within CECs. Furthermore, differential exon usage, pathway enrichment and spatial transcriptomics reveal TCF4 isoform ratio skewing solely in Exp+ FECD with potential downstream functional consequences. Lastly, exome data from 134 Exp- FECD cases identified rare (minor allele frequency <0.005) and potentially deleterious (CADD>15) TCF4 variants in 7/134 FECD Exp- cases, suggesting that TCF4 variants independent of CTG18.1 may increase FECD risk. In summary, our study supports the hypothesis that at least two distinct pathogenic mechanisms, RNA toxicity and TCF4 isoform-specific dysregulation, both underpin the pathophysiology of FECD. We anticipate these data will inform and guide the development of translational interventions for this common triplet-repeat mediated disease.
Collapse
Affiliation(s)
- Nihar Bhattacharyya
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Niuzheng Chai
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Amanda N. Sadan
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Anita Szabo
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Jana Jedlickova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Szi Kay Leung
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Tianyi Liao
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavlina Skalicka
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Mohit Parekh
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Ismail Moghul
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Aaron R. Jeffries
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Michael E. Cheetham
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Alison J. Hardcastle
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Nikolas Pontikos
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Stephen J. Tuft
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Alice E. Davidson
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| |
Collapse
|
4
|
Tam CS, Opat S, D'Sa S, Jurczak W, Lee HP, Cull G, Owen RG, Marlton P, Wahlin BE, García-Sanz R, McCarthy H, Mulligan S, Tedeschi A, Castillo JJ, Czyż J, Fernández De Larrea C, Belada D, Libby E, Matous J, Motta M, Siddiqi T, Tani M, Trněný M, Minnema MC, Buske C, Leblond V, Treon SP, Trotman J, Wu B, Yu Y, Shen Z, Chan WY, Schneider J, Allewelt H, Cohen A, Dimopoulos MA. Biomarker analysis of the ASPEN study comparing zanubrutinib with ibrutinib for patients with Waldenström macroglobulinemia. Blood Adv 2024; 8:1639-1650. [PMID: 38315878 PMCID: PMC11006814 DOI: 10.1182/bloodadvances.2023010906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 02/07/2024] Open
Abstract
ABSTRACT The phase 3 ASPEN trial (NCT03053440) compared Bruton tyrosine kinase inhibitors (BTKis), zanubrutinib and ibrutinib, in patients with Waldenström macroglobulinemia (WM). Post-hoc biomarker analysis was performed using next-generation sequencing on pretreatment bone marrow samples from 98 patients treated with zanubrutinib and 92 patients treated with ibrutinib with mutated (MUT) MYD88 and 20 patients with wild-type (WT) MYD88 treated with zanubrutinib. Of 329 mutations in 52 genes, mutations in CXCR4 (25.7%), TP53 (24.8%), ARID1A (15.7%), and TERT (9.0%) were most common. TP53MUT, ARID1AMUT, and TERTMUT were associated with higher rates of CXCR4MUT (P < .05). Patients with CXCR4MUT (frameshift or nonsense [NS] mutations) had lower very good partial response (VGPR) and complete response rates (CR; 17.0% vs 37.2%, P = .020) and longer time to response (11.1 vs 8.4 months) than patients with CXCR4WT treated with BTKis. CXCR4NS was associated with inferior progression-free survival (PFS; hazard ratio [HR], 3.39; P = .017) in patients treated with ibrutinib but not in those treated with zanubrutinib (HR, 0.67; P = .598), but VGPR + CR rates were similar between treatment groups (14.3% vs 15.4%). Compared with ibrutinib, patients with CXCR4NS treated with zanubrutinib had a favorable major response rate (MRR; 85.7% vs 53.8%; P = .09) and PFS (HR, 0.30; P = .093). In patients with TP53MUT, significantly lower MRRs were observed for patients treated with ibrutinib (63.6% vs 85.7%; P = .04) but not for those treated with zanubrutinib (80.8% vs 81.9%; P = .978). In TP53MUT, compared with ibrutinib, patients treated with zanubrutinib had higher VGPR and CR (34.6% vs 13.6%; P < .05), numerically improved MRR (80.8% vs 63.6%; P = .11), and longer PFS (not reached vs 44.2 months; HR, 0.66; P = .37). Collectively, patients with WM with CXCR4MUT or TP53MUT had worse prognosis compared with patients with WT alleles, and zanubrutinib led to better clinical outcomes.
Collapse
Affiliation(s)
- Constantine S. Tam
- Department of Haematology, Alfred Hospital and Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Stephen Opat
- Department of Haematology, Monash Health and Monash University, Clayton, VIC, Australia
| | - Shirley D'Sa
- Centre for Waldenström’s Macroglobulinemia and Associated Disorders, University College London Hospital Foundation Trust, London, United Kingdom
| | - Wojciech Jurczak
- Department of Clinical Oncology, Maria Sklodowska-Curie National Institute of Oncology, Krakow, Poland
| | - Hui-Peng Lee
- Department of Haematology, Flinders Medical Centre, Adelaide, SA, Australia
| | - Gavin Cull
- Department of Haematology, Sir Charles Gairdner Hospital, University of Western Australia, Perth, WA, Australia
| | - Roger G. Owen
- Haematological Malignancy Diagnostic Service, St James University Hospital, Leeds, United Kingdom
| | - Paula Marlton
- Department of Haematology, Princess Alexandra Hospital and University of Queensland, Brisbane, QLD, Australia
| | - Björn E. Wahlin
- Department of Hematology, Karolinska Universitetssjukhuset and Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Ramón García-Sanz
- Department of Hematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Helen McCarthy
- Department of Haematology, Royal Bournemouth and Christchurch Hospital, Bournemouth, United Kingdom
| | - Stephen Mulligan
- Department of Haematology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Alessandra Tedeschi
- Department of Hematology, Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Jorge J. Castillo
- Bing Center for Waldenstrom Macroglobulinemia, Dana-Farber Cancer Institute, Boston, MA
| | - Jarosław Czyż
- Department of Hematology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | | | - David Belada
- Department of Internal Medicine – Haematology, University Hospital and Faculty of Medicine, Hradec Králové, Czech Republic
| | - Edward Libby
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | - Marina Motta
- Department of Hematology, AO Spedali Civili di Brescia, Lombardia, Italy
| | - Tanya Siddiqi
- Department of Hematology/Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA
| | - Monica Tani
- U.O. Ematologia, Dipartimento Oncologia e Ematologia, Ospedale Civile Santa Maria delle Croci, AUSL Ravenna, Italy
| | - Marek Trněný
- Všeobecná fakultní nemocnice v Praze, Prague, Czechia
| | - Monique C. Minnema
- Department of Hematology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Christian Buske
- Comprehensive Cancer Center Ulm, Universitätsklinikum Ulm, Ulm, Baden-Württemberg, Germany
| | - Véronique Leblond
- Service d'Hématologie Clinique, Sorbonne University, Pitié Salpêtrière Hospital, Paris, France
| | - Steven P. Treon
- Bing Center for Waldenstrom Macroglobulinemia, Dana-Farber Cancer Institute, Boston, MA
| | - Judith Trotman
- Department of Hematology, Concord Repatriation General Hospital, Sydney, NSW, Australia
| | - Binghao Wu
- BeiGene USA, Inc, San Mateo, CA
- BeiGene Co, Ltd, Shanghai, China
| | - Yiling Yu
- BeiGene USA, Inc, San Mateo, CA
- BeiGene Co, Ltd, Shanghai, China
| | - Zhirong Shen
- BeiGene USA, Inc, San Mateo, CA
- BeiGene Co, Ltd, Shanghai, China
| | - Wai Y. Chan
- BeiGene USA, Inc, San Mateo, CA
- BeiGene Co, Ltd, Shanghai, China
| | | | | | - Aileen Cohen
- BeiGene USA, Inc, San Mateo, CA
- BeiGene Co, Ltd, Shanghai, China
| | - Meletios A. Dimopoulos
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
5
|
Benvenuto M, Cesarini S, Severi G, Ambrosini E, Russo A, Seri M, Palumbo P, Palumbo O, Castori M, Panza E, Carella M. Phenotypic Description of A Patient with ODLURO Syndrome and Functional Characterization of the Pathogenetic Role of A Synonymous Variant c.186G>A in KMT2E Gene. Genes (Basel) 2024; 15:430. [PMID: 38674365 PMCID: PMC11049644 DOI: 10.3390/genes15040430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
O'Donnell-Luria-Rodan (ODLURO) syndrome is an autosomal dominant disorder caused by mutations in the KMT2E gene. The clinical phonotype of the affected individuals is typically characterized by global developmental delay, autism, epilepsy, hypotonia, macrocephaly, and very mild dysmorphic facial features. In this report, we describe the case of a 6-year-old boy with ODLURO syndrome who is a carrier of the synonymous mutation c.186G>A (p.Ala62=) in the KMT2E gene, predicted to alter splicing by in silico tools. Given the lack of functional studies on the c.186G>A variant, in order to assess its potential functional effect, we sequenced the patient's cDNA demonstrating its impact on the mechanism of splicing. To the best of our knowledge, our patient is the second to date reported carrying this synonymous mutation, but he is the first whose functional investigation has confirmed the deleterious consequence of the variant, resulting in exon 4 skipping. Additionally, we suggest a potential etiological mechanism that could be responsible for the aberrant splicing mechanism in KMT2E.
Collapse
Affiliation(s)
- Mario Benvenuto
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (M.B.); (P.P.); (O.P.); (M.C.)
- Dipartimento degli Studi Umanistici, Università degli Studi di Foggia, 71122 Foggia, Italy
| | - Sofia Cesarini
- U.O.C. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (S.C.); (G.S.); (E.A.)
| | - Giulia Severi
- U.O.C. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (S.C.); (G.S.); (E.A.)
| | - Enrico Ambrosini
- U.O.C. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (S.C.); (G.S.); (E.A.)
| | - Angelo Russo
- U.O.C. Neuropsichiatria Infantile, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy;
| | - Marco Seri
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (M.S.); (E.P.)
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (M.B.); (P.P.); (O.P.); (M.C.)
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (M.B.); (P.P.); (O.P.); (M.C.)
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (M.B.); (P.P.); (O.P.); (M.C.)
| | - Emanuele Panza
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (M.S.); (E.P.)
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40126 Bologna, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (M.B.); (P.P.); (O.P.); (M.C.)
| |
Collapse
|
6
|
Mougeot JLC, Beckman MF, Alexander AS, Hovan AJ, Hasséus B, Legert KG, Johansson JE, von Bültzingslöwen I, Brennan MT, Mougeot FB. Single nucleotide polymorphisms conferring susceptibility to leukemia and oral mucositis: a multi-center pilot study of patients prior to conditioning therapy for hematopoietic cell transplant. Support Care Cancer 2024; 32:220. [PMID: 38467943 DOI: 10.1007/s00520-024-08408-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
PURPOSE Leukemias have been associated with oral manifestations, reflecting susceptibility to cancer therapy-induced oral mucositis. We sought to identify SNPs associated with both leukemia and oral mucositis (OM). METHODS Whole exome sequencing was performed on leukemia and non-cancer blood disorder (ncBD) patients' saliva samples (N = 50) prior to conditioning therapy. WHO OM grading scores were determined: moderate to severe (OM2-4) vs. none to mild (OM0-1). Reads were processed using Trim Galorev0.6.7, Bowtie2v2.4.1, Samtoolsv1.10, Genome Analysis Toolkit (GATK)v4.2.6.1, and DeepVariantv1.4.0. We utilized the following pipelines: P1 analysis with PLINK2v3.7, SNP2GENEv1.4.1 and MAGMAv1.07b, and P2 [leukemia (N = 42) vs. ncBDs (N = 8)] and P3 [leukemia + OM2-4 (N = 18) vs. leukemia + OM0-1 (N = 24)] with Z-tests of genotypes and protein-protein interaction determination. GeneCardsSuitev5.14 was used to identify phenotypes (P1 and P2, leukemia; P3, oral mucositis) and average disease-causing likelihood and DGIdb for drug interactions. P1 and P2 genes were analyzed with CytoScape plugin BiNGOv3.0.3 to retrieve overrepresented Gene Ontology (GO) terms and Ensembl's VEP for SNP outcomes. RESULTS In P1, 457 candidate SNPs (28 genes) were identified and 21,604 SNPs (1016 genes) by MAGMAv1.07b. Eighteen genes were associated with "leukemia" per VarElectv5.14 analysis and predicted to be deleterious. In P2 and P3, 353 and 174 SNPs were significant, respectively. STRINGv12.0 returned 77 and 32 genes (C.L. = 0.7) for P2 and P3, respectively. VarElectv5.14 determined 60 genes from P2 associated with "leukemia" and 11 with "oral mucositis" from P3. Overrepresented GO terms included "cellular process," "signaling," "hemopoiesis," and "regulation of immune response." CONCLUSIONS We identified candidate SNPs possibly conferring susceptibility to develop leukemia and oral mucositis.
Collapse
Affiliation(s)
- Jean-Luc C Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health Carolinas Medical Center, Charlotte, NC, USA.
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| | - Micaela F Beckman
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health Carolinas Medical Center, Charlotte, NC, USA
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Adam S Alexander
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health Carolinas Medical Center, Charlotte, NC, USA
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Allan J Hovan
- BC Cancer, Oral Oncology and Dentistry, Vancouver, BC, Canada
| | - Bengt Hasséus
- Department of Oral Medicine and Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Karin Garming Legert
- Department of Dental Medicine, University Dental Clinic, Karolinska Institutet, Huddinge, Sweden
| | - Jan-Erik Johansson
- Department of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Michael T Brennan
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health Carolinas Medical Center, Charlotte, NC, USA
| | - Farah Bahrani Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health Carolinas Medical Center, Charlotte, NC, USA.
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| |
Collapse
|
7
|
Wang Z, Zhao G, Zhu Z, Wang Y, Xiang X, Zhang S, Luo T, Zhou Q, Qiu J, Tang B, Xia K, Li B, Li J. VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome. Nucleic Acids Res 2024; 52:D1478-D1489. [PMID: 37956311 PMCID: PMC10767961 DOI: 10.1093/nar/gkad1061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
VarCards, an online database, combines comprehensive variant- and gene-level annotation data to streamline genetic counselling for coding variants. Recognising the increasing clinical relevance of non-coding variations, there has been an accelerated development of bioinformatics tools dedicated to interpreting non-coding variations, including single-nucleotide variants and copy number variations. Regrettably, most tools remain as either locally installed databases or command-line tools dispersed across diverse online platforms. Such a landscape poses inconveniences and challenges for genetic counsellors seeking to utilise these resources without advanced bioinformatics expertise. Consequently, we developed VarCards2, which incorporates nearly nine billion artificially generated single-nucleotide variants (including those from mitochondrial DNA) and compiles vital annotation information for genetic counselling based on ACMG-AMP variant-interpretation guidelines. These annotations include (I) functional effects; (II) minor allele frequencies; (III) comprehensive function and pathogenicity predictions covering all potential variants, such as non-synonymous substitutions, non-canonical splicing variants, and non-coding variations and (IV) gene-level information. Furthermore, VarCards2 incorporates 368 820 266 documented short insertions and deletions and 2 773 555 documented copy number variations, complemented by their corresponding annotation and prediction tools. In conclusion, VarCards2, by integrating over 150 variant- and gene-level annotation sources, significantly enhances the efficiency of genetic counselling and can be freely accessed at http://www.genemed.tech/varcards2/.
Collapse
Affiliation(s)
- Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhaopo Zhu
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Yijing Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xudong Xiang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shiyu Zhang
- Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jian Qiu
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, & Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| |
Collapse
|
8
|
Zhou Z, Kim J, Huang AY, Nolan M, Park J, Doan R, Shin T, Miller MB, Chhouk B, Morillo K, Yeh RC, Kenny C, Neil JE, Lee CZ, Ohkubo T, Ravits J, Ansorge O, Ostrow LW, Lagier-Tourenne C, Lee EA, Walsh CA. Somatic Mosaicism in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Reveals Widespread Degeneration from Focal Mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569436. [PMID: 38077003 PMCID: PMC10705414 DOI: 10.1101/2023.11.30.569436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Although mutations in dozens of genes have been implicated in familial forms of amyotrophic lateral sclerosis (fALS) and frontotemporal degeneration (fFTD), most cases of these conditions are sporadic (sALS and sFTD), with no family history, and their etiology remains obscure. We tested the hypothesis that somatic mosaic mutations, present in some but not all cells, might contribute in these cases, by performing ultra-deep, targeted sequencing of 88 genes associated with neurodegenerative diseases in postmortem brain and spinal cord samples from 404 individuals with sALS or sFTD and 144 controls. Known pathogenic germline mutations were found in 20.6% of ALS, and 26.5% of FTD cases. Predicted pathogenic somatic mutations in ALS/FTD genes were observed in 2.7% of sALS and sFTD cases that did not carry known pathogenic or novel germline mutations. Somatic mutations showed low variant allele fraction (typically <2%) and were often restricted to the region of initial discovery, preventing detection through genetic screening in peripheral tissues. Damaging somatic mutations were preferentially enriched in primary motor cortex of sALS and prefrontal cortex of sFTD, mirroring regions most severely affected in each disease. Somatic mutation analysis of bulk RNA-seq data from brain and spinal cord from an additional 143 sALS cases and 23 controls confirmed an overall enrichment of somatic mutations in sALS. Two adult sALS cases were identified bearing pathogenic somatic mutations in DYNC1H1 and LMNA, two genes associated with pediatric motor neuron degeneration. Our study suggests that somatic mutations in fALS/fFTD genes, and in genes associated with more severe diseases in the germline state, contribute to sALS and sFTD, and that mosaic mutations in a small fraction of cells in focal regions of the nervous system can ultimately result in widespread degeneration.
Collapse
Affiliation(s)
- Zinan Zhou
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Junho Kim
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - August Yue Huang
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Matthew Nolan
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Junseok Park
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ryan Doan
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Michael B. Miller
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian Chhouk
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Katherine Morillo
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rebecca C. Yeh
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Connor Kenny
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jennifer E. Neil
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
| | - Chao-Zong Lee
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Takuya Ohkubo
- Department of Neurology, Yokohama City Minato Red Cross Hospital, Yokohama, Kanagawa, Japan
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, Oxfordshire, UK
| | - Lyle W. Ostrow
- Department of Neurology, Lewis Katz School of Medicine at Temple University, Philadelphia, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
| |
Collapse
|
9
|
Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data 2023; 10:813. [PMID: 37985666 PMCID: PMC10662356 DOI: 10.1038/s41597-023-02645-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, which include >400 terabytes of data from 1087 subjects, are now available to the research community via the NIMH Data Archive (NDA) and are described here.
Collapse
Affiliation(s)
- McKinzie A Garrison
- Program in Biochemistry, Molecular and Cellular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Attila Jones
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Cindy Molitor
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle, WA, 98121, USA
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mette A Peters
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle, WA, 98121, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Xiaoxu Yang
- Rady Children's Institute for Genomic Medicine, 7910 Frost St., Suite #300, San Diego, CA, 92123, USA
- Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Chess
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred H Gage
- Laboratory of Genetics LOG-G, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, 7910 Frost St., Suite #300, San Diego, CA, 92123, USA
- Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | | | - Ryan E Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Flora M Vaccarino
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sarah J Wheelan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- National Human Genome Research Institute, National Institutes of Health, 6700B Rockledge Dr, Bethesda, MD, 20892, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
| |
Collapse
|
10
|
Lokki AI, Ren Z, Triebwasser M, Daly E, Perola M, Auro K, Burwick R, Salmon JE, Daly M, Laivuori H, Atkinson JP, Java A, Meri S. Identification of complement factor H variants that predispose to pre-eclampsia: A genetic and functional study. BJOG 2023; 130:1473-1482. [PMID: 37156755 PMCID: PMC10592561 DOI: 10.1111/1471-0528.17529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
OBJECTIVE The objective of the study was to investigate the role of genetic variants in complement proteins in pre-eclampsia. DESIGN In a case-control study involving 609 cases and 2092 controls, five rare variants in complement factor H (CFH) were identified in women with severe and complicated pre-eclampsia. No variants were identified in controls. SETTING Pre-eclampsia is a leading cause of maternal and fetal morbidity and mortality. Immune maladaptation, in particular, complement activation that disrupts maternal-fetal tolerance leading to placental dysfunction and endothelial injury, has been proposed as a pathogenetic mechanism, but this remains unproven. POPULATION We genotyped 609 pre-eclampsia cases and 2092 controls from FINNPEC and the national FINRISK cohorts. METHODS Complement-based functional and structural assays were conducted in vitro to define the significance of these five missense variants and each compared with wild type. MAIN OUTCOME MEASURES Secretion, expression and ability to regulate complement activation were assessed for factor H proteins harbouring the mutations. RESULTS We identified five heterozygous rare variants in complement factor H (L3V, R127H, R166Q, C1077S and N1176K) in seven women with severe pre-eclampsia. These variants were not identified in controls. Variants C1077S and N1176K were novel. Antigenic, functional and structural analyses established that four (R127H, R166Q, C1077S and N1176K) were deleterious. Variants R127H and C1077S were synthesised, but not secreted. Variants R166Q and N1176K were secreted normally but showed reduced binding to C3b and consequently defective complement regulatory activity. No defect was identified for L3V. CONCLUSIONS These results suggest that complement dysregulation due to mutations in complement factor H is among the pathophysiological mechanisms underlying severe pre-eclampsia.
Collapse
Affiliation(s)
- A Inkeri Lokki
- Immunobiology Research Program, Bacteriology and Immunology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Heart and Lung Centre, Helsinki University Hospital, Helsinki, Finland
| | - Zhen Ren
- Division of Clinical Immunology and Allergy, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael Triebwasser
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Emma Daly
- Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Markus Perola
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Kirsi Auro
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Richard Burwick
- Maternal Fetal Medicine, San Gabriel Valley Perinatal Medical Group, Pomona Valley Hospital Medical Center, Pomona, California, USA
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jane E Salmon
- Hospital for Special Surgery, Weill Medical College of Cornell University, New York, New York, USA
| | - Mark Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Hannele Laivuori
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynaecology, Tampere University Hospital, Tampere University, Tampere, Finland
- Centre for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - John P Atkinson
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Anuja Java
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Seppo Meri
- Immunobiology Research Program, Bacteriology and Immunology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- HUSLAB Diagnostic Centre, Helsinki University Hospital, Helsinki, Finland
| |
Collapse
|
11
|
Benvenuto M, Palumbo P, Di Muro E, Perrotta CS, Mazza T, Mandarà GML, Palumbo O, Carella M. Identification of a Novel FOXP1 Variant in a Patient with Hypotonia, Intellectual Disability, and Severe Speech Impairment. Genes (Basel) 2023; 14:1958. [PMID: 37895307 PMCID: PMC10606110 DOI: 10.3390/genes14101958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The FOXP subfamily includes four different transcription factors: FOXP1, FOXP2, FOXP3, and FOXP4, all with important roles in regulating gene expression from early development through adulthood. Haploinsufficiency of FOXP1, due to deleterious variants (point mutations, copy number variants) disrupting the gene, leads to an emerging disorder known as "FOXP1 syndrome", mainly characterized by intellectual disability, language impairment, dysmorphic features, and multiple congenital abnormalities with or without autistic features in some affected individuals (MIM 613670). Here we describe a 10-year-old female patient, born to unrelated parents, showing hypotonia, intellectual disability, and severe language delay. Targeted resequencing analysis allowed us to identify a heterozygous de novo FOXP1 variant c.1030C>T, p.(Gln344Ter) classified as likely pathogenetic according to the American College of Medical Genetics and Genomics guidelines. To the best of our knowledge, our patient is the first to date to report carrying this stop mutation, which is, for this reason, useful for broadening the molecular spectrum of FOXP1 clinically relevant variants. In addition, our results highlight the utility of next-generation sequencing in establishing an etiological basis for heterogeneous conditions such as neurodevelopmental disorders and providing additional insight into the phenotypic features of FOXP1-related syndrome.
Collapse
Affiliation(s)
- Mario Benvenuto
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
- Dipartimento Degli Studi Umanistici, Università Degli Studi di Foggia, 71122 Foggia, Italy
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
| | - Ester Di Muro
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
| | | | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy;
| | | | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy; (M.B.); (P.P.); (E.D.M.); (O.P.)
| |
Collapse
|
12
|
Zang J, Zhang R, Jin D, Xie F, Shahatiaili A, Wu G, Zhang Y, Zhao Z, Du P, Jia S, Chen H, Zhuang G. Integrated longitudinal circulating tumor DNA profiling predicts immunotherapy response of metastatic urothelial carcinoma in the POLARIS-03 trial. J Pathol 2023; 261:198-209. [PMID: 37584165 DOI: 10.1002/path.6166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 08/17/2023]
Abstract
Non-invasive biomarkers for immunotherapy response remain a compelling unmet medical need. POLARIS-03 is a multicenter phase II trial to evaluate the safety and efficacy of toripalimab (anti-programmed cell death 1) in refractory metastatic urothelial carcinoma (mUC). We assessed the predictive utility of longitudinal circulating tumor DNA (ctDNA) analysis from a single-institution biomarker cohort. Twenty-seven mUC patients receiving toripalimab (3 mg/kg Q2W) at Ren Ji Hospital were enrolled. Serial plasma specimens were obtained at baseline and then every two cycles during treatment. The 600-gene panel (PredicineATLAS™) liquid biopsy assay was applied to probe somatic variants and cancer cell fraction (CCF). Low-pass whole genome sequencing was used to determine the copy number abnormality (CNA) score. Across the entire cohort, we observed different degrees of concordance between somatic aberrations detected by ctDNA and those inferred by matched tumor samples. Although the baseline CCF or CNA had limited predictive value, early ctDNA response at week 8 was associated with toripalimab efficacy and prolonged patient survival. Integrating CCF and CNA decrease achieved a superior accuracy of 90.5% in classifying responders and non-responders and predicted long-term benefit from toripalimab. Dynamic changes in the CCF and CNA in blood exquisitely reflected radiographic assessment of malignant lesions, including those with FGFR3-TACC3 gene fusion or microsatellite instability. This study demonstrates the feasibility and effectiveness of integrated longitudinal ctDNA profiling as a potential biomarker in mUC patients undergoing immunotherapy and supports further clinical evaluation of minimally invasive liquid biopsy assays for treatment stratification and therapy monitoring. © 2023 The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Jingyu Zang
- State Key Laboratory of Systems Medicine for Cancer, Department of Radiation Oncology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Ruiyun Zhang
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Di Jin
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Feng Xie
- Huidu Shanghai Medical Sciences Ltd, Shanghai, PR China
| | - Akezhouli Shahatiaili
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Guangyu Wu
- Department of Imaging, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Yue Zhang
- Huidu Shanghai Medical Sciences Ltd, Shanghai, PR China
| | | | - Pan Du
- Predicine, Inc., Hayward, CA, USA
| | - Shidong Jia
- Huidu Shanghai Medical Sciences Ltd, Shanghai, PR China
| | - Haige Chen
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Guanglei Zhuang
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| |
Collapse
|
13
|
Mougeot JLC, Beckman MF, Hovan AJ, Hasséus B, Legert KG, Johansson JE, von Bültzingslöwen I, Brennan MT, Bahrani Mougeot F. Identification of single nucleotide polymorphisms (SNPs) associated with chronic graft-versus-host disease in patients undergoing allogeneic hematopoietic cell transplantation. Support Care Cancer 2023; 31:587. [PMID: 37731134 PMCID: PMC10511391 DOI: 10.1007/s00520-023-08044-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
INTRODUCTION Chronic graft-versus-host disease (cGVHD) is a debilitating side effect of allogeneic hematopoietic cell transplantation (HCT), affecting the quality of life of patients. We used whole exome sequencing to identify candidate SNPs and complete a multi-marker gene-level analysis using a cohort of cGVHD( +) (N = 16) and cGVHD( -) (N = 66) HCT patients. METHODS Saliva samples were collected from HCT patients (N = 82) pre-conditioning in a multi-center study from March 2011 to May 2018. Exome sequencing was performed and FASTQ files were processed for sequence alignments. Significant SNPs were identified by logistic regression using PLINK2v3.7 and Fisher's exact test. One cGVHD( -) patient sample was excluded from further analysis since no SNP was present in at least 10% of the sample population. The FUMA platform's SNP2GENE was utilized to annotate SNPs and generate a MAGMA output. Chromatin state visualization of lead SNPs was completed using Epilogos tool. FUMA's GENE2FUNC was used to obtain gene function and tissue expression from lead genomic loci. RESULTS Logistic regression classified 986 SNPs associated with cGVHD( +). SNP2GENE returned three genomic risk loci, four lead SNPs, 48 candidate SNPs, seven candidate GWAS tagged SNPs, and four mapped genes. Fisher's exact test identified significant homozygous genotypes of four lead SNPs (p < 0.05). GENE2FUNC analysis of multi-marker SNP sets identified one positional gene set including lead SNPs for KANK1 and KDM4C and two curated gene sets including lead SNPs for PTPRD, KDM4C, and/or KANK1. CONCLUSIONS Our data suggest that SNPs in three genes located on chromosome 9 confer genetic susceptibility to cGVHD in HCT patients. These genes modulate STAT3 expression and phosphorylation in cancer pathogenesis. The findings may have implications in the modulation of pathways currently targeted by JAK inhibitors in cGVHD clinical trials.
Collapse
Affiliation(s)
- Jean-Luc C Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA.
| | - Micaela F Beckman
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA
| | - Allan J Hovan
- BC Cancer, Oral Oncology and Dentistry, Vancouver, BC, Canada
| | - Bengt Hasséus
- Department of Oral Medicine and Pathology, University of Gothenburg, Gothenburg, Sweden
| | | | - Jan-Erik Johansson
- Department of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Michael T Brennan
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Farah Bahrani Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA.
| |
Collapse
|
14
|
Maryami F, Rismani E, Davoudi-Dehaghani E, Khalesi N, Talebi S, Mahdian R, Zeinali S. In silico Analysis of Two Novel Variants in the Pyruvate Carboxylase (PC) Gene Associated with the Severe Form of PC Deficiency. IRANIAN BIOMEDICAL JOURNAL 2023; 27:307-19. [PMID: 37873728 PMCID: PMC10707810 DOI: 10.61186/ibj.27.5.307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/17/2023] [Indexed: 12/17/2023]
Abstract
Background Inborne errors of metabolism are a common cause of neonatal death. This study evaluated the acute early-onset metabolic derangement and death in two unrelated neonates. Methods Whole-exome sequencing (WES), Sanger sequencing, homology modeling, and in silico bioinformatics analysis were employed to assess the effects of variants on protein structure and function. Results WES revealed a novel homozygous variant, p.G303Afs*40 and p.R156P, in the pyruvate carboxylase (PC) gene of each neonate, which both were confirmed by Sanger sequencing. Based on the American College of Medical Genetics and Genomics guidelines, the p.G303Afs*40 was likely pathogenic, and the p.R156P was a variant of uncertain significance (VUS). Nevertheless, a known variant at position 156, the p.R156Q, was also a VUS. Protein secondary structure prediction showed changes in p.R156P and p.R156Q variants compared to the wild-type protein. However, p.G303Afs*40 depicted significant changes at C-terminal. Furthermore, comparing the interaction of wild-type and variant proteins with the ATP ligand during simulations, revealed a decreased affinity to the ATP in all the variants. Moreover, analysis of Single nucleotide polymorphism impacts on PC protein using Polyphen-2, SNAP2, FATHMM, and SNPs&GO servers predicted both R156P and R156Q as damaging variants. Likewise, free energy calculations demonstrated the destabilizing effect of both variants on PC. Conclusion This study confirmed the pathogenicity of both variants and suggested them as a cause of type B Pyruvate carboxylase deficiency. The results of this study would provide the family with prenatal diagnosis and expand the variant spectrum in the PC gene,which is beneficial for geneticists and endocrinologists.
Collapse
Affiliation(s)
- Fereshteh Maryami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Rismani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Nasrin Khalesi
- Department of Pediatrics and Neonatal Intensive Care Unit, Ali-Asghar Children’s Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Reza Mahdian
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
- Kawsar Human Genetics Research Center, Tehran, Iran
| |
Collapse
|
15
|
Choi J, Kim S, Kim J, Son HY, Yoo SK, Kim CU, Park YJ, Moon S, Cha B, Jeon MC, Park K, Yun JM, Cho B, Kim N, Kim C, Kwon NJ, Park YJ, Matsuda F, Momozawa Y, Kubo M, Kim HJ, Park JH, Seo JS, Kim JI, Im SW. A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants. SCIENCE ADVANCES 2023; 9:eadg6319. [PMID: 37556544 PMCID: PMC10411914 DOI: 10.1126/sciadv.adg6319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
Abstract
Underrepresentation of non-European (EUR) populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72,298 subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East Asian specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell type-specific effects. We suggest that this dataset will add to the potential value of Asian precision medicine.
Collapse
Affiliation(s)
- Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Juhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ho-Young Son
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Young Jun Park
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sungji Moon
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Bukyoung Cha
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Min Chul Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyunghyuk Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jae Moon Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Belong Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | | | | | - Young Joo Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Hyun-Jin Kim
- National Cancer Control Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong-Sun Seo
- Macrogen Inc., Seoul, Republic of Korea
- Asian Genome Center, Seoul National University Bundang Hospital, Gyeonggi, Republic of Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun-Wha Im
- Department of Biochemistry and Molecular Biology, Kangwon National University School of Medicine, Gangwon, Republic of Korea
| |
Collapse
|
16
|
Tafazoli A, Mikros J, Khaghani F, Alimardani M, Rafigh M, Hemmati M, Siamoglou S, Golińska AK, Kamiński KA, Niemira M, Miltyk W, Patrinos GP. Pharmacovariome scanning using whole pharmacogene resequencing coupled with deep computational analysis and machine learning for clinical pharmacogenomics. Hum Genomics 2023; 17:62. [PMID: 37452347 PMCID: PMC10347842 DOI: 10.1186/s40246-023-00508-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND This pilot study aims to identify and functionally assess pharmacovariants in whole exome sequencing data. While detection of known variants has benefited from pharmacogenomic-dedicated bioinformatics tools before, in this paper we have tested novel deep computational analysis in addition to artificial intelligence as possible approaches for functional analysis of unknown markers within less studied drug-related genes. METHODS Pharmacovariants from 1800 drug-related genes from 100 WES data files underwent (a) deep computational analysis by eight bioinformatic algorithms (overall containing 23 tools) and (b) random forest (RF) classifier as the machine learning (ML) approach separately. ML model efficiency was calculated by internal and external cross-validation during recursive feature elimination. Protein modelling was also performed for predicted highly damaging variants with lower frequencies. Genotype-phenotype correlations were implemented for top selected variants in terms of highest possibility of being damaging. RESULTS Five deleterious pharmacovariants in the RYR1, POLG, ANXA11, CCNH, and CDH23 genes identified in step (a) and subsequent analysis displayed high impact on drug-related phenotypes. Also, the utilization of recursive feature elimination achieved a subset of 175 malfunction pharmacovariants in 135 drug-related genes that were used by the RF model with fivefold internal cross-validation, resulting in an area under the curve of 0.9736842 with an average accuracy of 0.9818 (95% CI: 0.89, 0.99) on predicting whether a carrying individuals will develop adverse drug reactions or not. However, the external cross-validation of the same model indicated a possible false positive result when dealing with a low number of observations, as only 60 important variants in 49 genes were displayed, giving an AUC of 0.5384848 with an average accuracy of 0.9512 (95% CI: 0.83, 0.99). CONCLUSION While there are some technologies for functionally assess not-interpreted pharmacovariants, there is still an essential need for the development of tools, methods, and algorithms which are able to provide a functional prediction for every single pharmacovariant in both large-scale datasets and small cohorts. Our approaches may bring new insights for choosing the right computational assessment algorithms out of high throughput DNA sequencing data from small cohorts to be used for personalized drug therapy implementation.
Collapse
Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Białystok, Poland
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Kraków, Poland
| | - John Mikros
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Faeze Khaghani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Guilan University of Medical Sciences, Rasht, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobeh Rafigh
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobeh Hemmati
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | | | - Karol A Kamiński
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Białystok, Poland
- Department of Cardiology, Medical University of Bialystok, Białystok, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, Białystok, Poland
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Białystok, Poland.
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
- Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
| |
Collapse
|
17
|
Gracia-Diaz C, Zhou Y, Yang Q, Maroofian R, Espana-Bonilla P, Lee CH, Zhang S, Padilla N, Fueyo R, Waxman EA, Lei S, Otrimski G, Li D, Sheppard SE, Mark P, Harr MH, Hakonarson H, Rodan L, Jackson A, Vasudevan P, Powel C, Mohammed S, Maddirevula S, Alzaidan H, Faqeih EA, Efthymiou S, Turchetti V, Rahman F, Maqbool S, Salpietro V, Ibrahim SH, di Rosa G, Houlden H, Alharbi MN, Al-Sannaa NA, Bauer P, Zifarelli G, Estaras C, Hurst ACE, Thompson ML, Chassevent A, Smith-Hicks CL, de la Cruz X, Holtz AM, Elloumi HZ, Hajianpour MJ, Rieubland C, Braun D, Banka S, French DL, Heller EA, Saade M, Song H, Ming GL, Alkuraya FS, Agrawal PB, Reinberg D, Bhoj EJ, Martínez-Balbás MA, Akizu N. Gain and loss of function variants in EZH1 disrupt neurogenesis and cause dominant and recessive neurodevelopmental disorders. Nat Commun 2023; 14:4109. [PMID: 37433783 PMCID: PMC10336078 DOI: 10.1038/s41467-023-39645-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Genetic variants in chromatin regulators are frequently found in neurodevelopmental disorders, but their effect in disease etiology is rarely determined. Here, we uncover and functionally define pathogenic variants in the chromatin modifier EZH1 as the cause of dominant and recessive neurodevelopmental disorders in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 methyltransferases of the PRC2 complex. Unlike the other PRC2 subunits, which are involved in cancers and developmental syndromes, the implication of EZH1 in human development and disease is largely unknown. Using cellular and biochemical studies, we demonstrate that recessive variants impair EZH1 expression causing loss of function effects, while dominant variants are missense mutations that affect evolutionarily conserved aminoacids, likely impacting EZH1 structure or function. Accordingly, we found increased methyltransferase activity leading to gain of function of two EZH1 missense variants. Furthermore, we show that EZH1 is necessary and sufficient for differentiation of neural progenitor cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell-derived neural cultures and forebrain organoids, we demonstrate that EZH1 variants perturb cortical neuron differentiation. Overall, our work reveals a critical role of EZH1 in neurogenesis regulation and provides molecular diagnosis for previously undefined neurodevelopmental disorders.
Collapse
Affiliation(s)
- Carolina Gracia-Diaz
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yijing Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qian Yang
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Paula Espana-Bonilla
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Chul-Hwan Lee
- Department of Biomedical Sciences and Pharmacology, Seoul National University, College of Medicine, Seoul, South Korea
| | - Shuo Zhang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Natàlia Padilla
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Raquel Fueyo
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Elisa A Waxman
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sunyimeng Lei
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Garrett Otrimski
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah E Sheppard
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul Mark
- Department of Pediatrics, Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Margaret H Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lance Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Pradeep Vasudevan
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK
| | - Corrina Powel
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK
| | | | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hamad Alzaidan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Valentina Turchetti
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Fatima Rahman
- Developmental and Behavioral Pediatrics, University of Child Health Sciences & The Children's Hospital, Lahore, Pakistan
| | - Shazia Maqbool
- Developmental and Behavioral Pediatrics, University of Child Health Sciences & The Children's Hospital, Lahore, Pakistan
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Shahnaz H Ibrahim
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Gabriella di Rosa
- Child Neuropsychiatry Unit, Department of Pediatrics, University of Messina, Messina, 98100, Italy
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Maha Nasser Alharbi
- Maternity and Children Hospital Buraidah, Qassim Health Cluster, Buraydah, Saudi Arabia
| | | | | | | | - Conchi Estaras
- Center for Translational Medicine, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA, USA
| | - Anna C E Hurst
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Anna Chassevent
- Department of Neurogenetics, Neurology and Developmental Medicine Kennedy Krieger Institute, Baltimore, MD, USA
| | - Constance L Smith-Hicks
- Department of Neurogenetics, Neurology and Developmental Medicine Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alexander M Holtz
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - M J Hajianpour
- Division of Medical Genetics and Genomics, Department of Pediatrics, Albany Medical College, Albany, NY, USA
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Dominique Braun
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Deborah L French
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Murielle Saade
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Pankaj B Agrawal
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Division of Neonatology, Department of Pediatrics, University of Miami School of Medicine and Holtz Children's Hospital, Jackson Heath System, Miami, FL, USA
| | | | - Elizabeth J Bhoj
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marian A Martínez-Balbás
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
18
|
Maryami F, Davoudi-Dehaghani E, Khalesi N, Rismani E, Rahimi H, Talebi S, Zeinali S. Identification and characterization of the largest deletion in the PCCA gene causing severe acute early-onset form of propionic acidemia. Mol Genet Genomics 2023; 298:905-917. [PMID: 37131081 DOI: 10.1007/s00438-023-02023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 04/16/2023] [Indexed: 05/04/2023]
Abstract
Whole-exome sequencing (WES) is an excellent method for the diagnosis of diseases of uncertain or heterogeneous genetic origin. However, it has limitations for detecting structural variations such as InDels, which the bioinformatics analyzers must be aware of. This study aimed at using WES to evaluate the genetic cause of the metabolic crisis in a 3-day-old neonate admitted to the neonatal intensive care unit (NICU) and deceased after a few days. Tandem mass spectrometry (MS/MS) showed a significant increase in propionyl carnitine (C3), proposing methylmalonic acidemia (MMA) or propionic acidemia (PA). WES demonstrated a homozygous missense variant in exon 4 of the BTD gene (NM_000060.4(BTD):c.1330G > C), responsible for partial biotinidase deficiency. Segregation analysis of the BTD variant revealed the homozygous status of the asymptomatic mother. Furthermore, observation of the bam file, around genes responsible for PA or MMA, by Integrative Genomics Viewer (IGV) software displayed a homozygous large deletion in the PCCA gene. Comprehensive confirmatory studies identified and segregated a novel outframe deletion of 217,877 bp length, "NG_008768.1:g.185211_403087delinsTA", extended from intron 11 to 21 of the PCCA, inducing a premature termination codon and activation of nonsense-mediated mRNA decay (NMD). Homology modeling of the mutant PCCA demonstrated eliminating the protein's active site and critical functional domains. Thereupon, this novel variant is suggested as the largest deletion in the PCCA gene, causing an acute early-onset PA. These results could expand the PCCA variants spectrum, and improve the existing knowledge on the molecular basis of PA, as well as provide new evidence of pathogenicity of the variant (NM_000060.4(BTD):c.1330G > C.
Collapse
Affiliation(s)
- Fereshteh Maryami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Nasrin Khalesi
- Department of Pediatrics and Neonatal Intensive Care Unit, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Shahid Vahid Dastgerdi Street, Modarres Highway, Tehran, Iran.
| | - Elham Rismani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
- Texas Biomedical Research Center, San Antonio, USA
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Medical Genetics, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran.
- Medical Genetics Lab, Kawsar Human Genetics Research Center, No. 41 Majlesi St., ValiAsr St., 1595645513, Tehran, Iran.
- Iranian Molecular Medicine Network, Pasteur Institute of Iran, Pasteur St, Tehran, Iran.
| |
Collapse
|
19
|
Maryami F, Rismani E, Davoudi-Dehaghani E, Khalesi N, Motlagh FZ, Kordafshari A, Talebi S, Rahimi H, Zeinali S. Identifying and predicting the pathogenic effects of a novel variant inducing severe early onset MMA: a bioinformatics approach. Hereditas 2023; 160:25. [PMID: 37248539 DOI: 10.1186/s41065-023-00281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Methylmalonic acidemia (MMA) is a rare metabolic disorder resulting from functional defects in methylmalonyl-CoA mutase. Mutations in the MMAB gene are responsible for the cblB type of vitamin B12-responsive MMA. RESULTS This study used Whole-exome sequencing (WES), Sanger sequencing, linkage analysis, and in-silico evaluation of the variants' effect on protein structure and function to confirm their pathogenicity in a 2-day-old neonate presenting an early-onset metabolic crisis and death. WES revealed a homozygous missense variant on chromosome 12, the NM_052845.4 (MMAB):c.557G > A, p.Arg186Gln, in exon 7, a highly conserved and hot spot region for pathogenic variants. After being confirmed by Sanger sequencing, the wild-type and mutant proteins' structure and function were modeled and examined using in-silico bioinformatics tools and compared to the variant NM_052845.4 (MMAB):c.556C > T, p.Arg186Trp, a known pathogenic variant at the same position. Comprehensive bioinformatics analysis showed a significant reduction in the stability of variants and changes in protein-protein and ligand-protein interactions. Interestingly, the variant c.557G > A, p.Arg186Gln depicted more variations in the secondary structure and less binding to the ATP and B12 ligands compared to the c.556C > T, p.Arg186Trp, the known pathogenic variant. CONCLUSION This study succeeded in expanding the variant spectra of the MMAB, forasmuch as the variant c.557G > A, p.Arg186Gln is suggested as a pathogenic variant and the cause of severe MMA and neonatal death. These results benefit the prenatal diagnosis of MMA in the subsequent pregnancies and carrier screening of the family members. Furthermore, as an auxiliary technique, homology modeling and protein structure and function evaluations could provide geneticists with a more accurate interpretation of variants' pathogenicity.
Collapse
Affiliation(s)
- Fereshteh Maryami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Rismani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Nasrin Khalesi
- Department of Pediatrics and Neonatal Intensive Care Unit, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Vahid Dastgerdi Street, Modarres Highway, Tehran, Iran.
| | | | - Alireza Kordafshari
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Medical Genetics, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
- Present address: Texas Biomedical Research Center, San Antonio, USA
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran.
- Medical Genetics Lab, Kawsar Human Genetics Research Center, No. 41 Majlesi St., ValiAsr St., Tehran, Iran.
| |
Collapse
|
20
|
Raggio V, Graña M, Winiarski E, Mansilla S, Simoes C, Rodríguez S, Brandes M, Tapié A, Rodríguez L, Cibils L, Alonso M, Martínez J, Fernández-Calero T, Domínguez F, Mezquida MR, Castro L, Cerisola A, Naya H, Cassina A, Quijano C, Spangenberg L. Computational and mitochondrial functional studies of novel compound heterozygous variants in SPATA5 gene support a causal link with epileptogenic encephalopathy. Hum Genomics 2023; 17:14. [PMID: 36849973 PMCID: PMC9972848 DOI: 10.1186/s40246-023-00463-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/20/2023] [Indexed: 03/01/2023] Open
Abstract
The SPATA5 gene encodes a 892 amino-acids long protein that has a putative mitochondrial targeting sequence and has been proposed to function in maintenance of mitochondrial function and integrity during mouse spermatogenesis. Several studies have associated homozygous or compound heterozygous mutations in SPATA5 gene to microcephaly, intellectual disability, seizures and hearing loss. This suggests a role of the SPATA5 gene also in neuronal development. Recently, our group presented results validating the use of blood cells for the assessment of mitochondrial function for diagnosis and follow-up of mitochondrial disease, minimizing the need for invasive procedures such as muscle biopsy. In this study, we were able to diagnose a patient with epileptogenic encephalopathy using next generation sequencing. We found two novel compound heterozygous variants in SPATA5 that are most likely causative. To analyze the impact of SPATA5 mutations on mitochondrial functional studies directly on the patients' mononuclear cells and platelets were undertaken. Oxygen consumption rates in platelets and PBMCs were impaired in the patient when compared to a healthy control. Also, a decrease in mitochondrial mass was observed in the patient monocytes with respect to the control. This suggests a true pathogenic effect of the mutations in mitochondrial function, especially in energy production and possibly biogenesis, leading to the observed phenotype.
Collapse
Affiliation(s)
- Víctor Raggio
- grid.11630.350000000121657640Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Martín Graña
- grid.418532.90000 0004 0403 6035Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Erik Winiarski
- grid.11630.350000000121657640Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Santiago Mansilla
- grid.11630.350000000121657640Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | - Camila Simoes
- grid.418532.90000 0004 0403 6035Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento Básico de Medicina, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Soledad Rodríguez
- grid.11630.350000000121657640Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mariana Brandes
- grid.418532.90000 0004 0403 6035Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandra Tapié
- grid.11630.350000000121657640Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Laura Rodríguez
- grid.11630.350000000121657640Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Lucía Cibils
- grid.11630.350000000121657640Departamento de Neuropediatría, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Martina Alonso
- grid.11630.350000000121657640Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jennyfer Martínez
- grid.11630.350000000121657640Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Tamara Fernández-Calero
- grid.418532.90000 0004 0403 6035Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.442041.70000 0001 2188 793XDepartment of Exact and Natural Sciences, Universidad Católica del Uruguay, 11600 Montevideo, Uruguay
| | - Fernanda Domínguez
- grid.11630.350000000121657640Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay ,grid.442041.70000 0001 2188 793XUniversidad Católica del Uruguay, 11600 Montevideo, Uruguay
| | - Melania Rosas Mezquida
- grid.11630.350000000121657640Departamento de Neuropediatría, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Laura Castro
- grid.11630.350000000121657640Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Alfredo Cerisola
- grid.11630.350000000121657640Departamento de Neuropediatría, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Hugo Naya
- grid.418532.90000 0004 0403 6035Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Adriana Cassina
- grid.11630.350000000121657640Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Celia Quijano
- grid.11630.350000000121657640Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Lucía Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay. .,Departamento Básico de Medicina, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| |
Collapse
|
21
|
Almandil NB, Alismail MA, Alsuwat HS, AlSulaiman A, AbdulAzeez S, Borgio JF. Exome-wide analysis identify multiple variations in olfactory receptor genes ( OR12D2 and OR5V1) associated with autism spectrum disorder in Saudi females. Front Med (Lausanne) 2023; 10:1051039. [PMID: 36817779 PMCID: PMC9928728 DOI: 10.3389/fmed.2023.1051039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/13/2023] [Indexed: 02/04/2023] Open
Abstract
Background Autism Spectrum Disorder (ASD) is a multifactorial, neurodevelopmental disorder, characterized by deficits in communication, restricted and repetitive behaviors. ASD is highly heritable in Saudi Arabia; indecencies of affected individuals are increasing. Objectives To identify the most significant genes and SNPs associated with the increased risk of ASD in Saudi females to give an insight for early diagnosis. Methods Pilot case-control study mostly emphasized on the significant SNPs and haplotypes contributing to Saudi females with ASD patients (n = 22) compared to controls (n = 51) without ASD. With the use of allelic association analysis tools, 243,345 SNPs were studied systematically and classified according to their significant association. The significant SNPs and their genes were selected for further investigation for mapping of ASD candidate causal variants and functional impact. Results In females, five risk SNPs at p ≤ 2.32 × 10-05 was identified in association with autism. The most significant exonic variants at chromosome 6p22.1 with olfactory receptor genes (OR12D2 and OR5V1) clustered with high linkage disequilibrium through haplotyping analysis. Comparison between highly associated genes (56 genes) of male and female autistic patients with female autistic samples revealed that 39 genes are unique biomarkers for Saudi females with ASD. Conclusion Multiple variations in olfactory receptor genes (OR5V1 and OR12D2) and single variations on SPHK1, PLCL2, AKAP9 and LOC107984893 genes are contributing to ASD in females of Arab origin. Accumulation of these multiple predisposed coding SNPs can increase the possibility of developing ASD in Saudi females.
Collapse
Affiliation(s)
- Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia,*Correspondence: Noor B Almandil,
| | - Maram Adnan Alismail
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia,College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Hind Saleh Alsuwat
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdulla AlSulaiman
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| |
Collapse
|
22
|
Hussain A, Acharya A, Bharadwaj T, Genomics UOWCFM, Leal SM, Khaliq A, Mir A, Schrauwen I. A Novel Variant in VPS13B Underlying Cohen Syndrome. BIOMED RESEARCH INTERNATIONAL 2023; 2023:9993801. [PMID: 37090188 PMCID: PMC10115529 DOI: 10.1155/2023/9993801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/15/2023] [Accepted: 03/03/2023] [Indexed: 04/25/2023]
Abstract
Pathogenic variants in vacuolar protein sorting 13 homolog B (VPS13B) cause Cohen syndrome (CS), a clinically diverse neurodevelopmental disorder. We used whole exome and Sanger sequencing to identify disease-causing variants in a Pakistani family with intellectual disability, microcephaly, facial dysmorphism, neutropenia, truncal obesity, speech delay, motor delay, and insomnia. We identified a novel homozygous nonsense variant c.8841G > A: p.(W2947∗) in VPS13B (NM_017890.5) which segregated with the disease. Sleep disturbances are commonly seen in neurodevelopmental disorders and can exacerbate medical issues if left untreated. We demonstrate that individuals with Cohen syndrome may also be affected by sleep disturbances. In conclusion, we expand the genetic and phenotypic features of Cohen syndrome in the Pakistani population.
Collapse
Affiliation(s)
- Abrar Hussain
- Human Molecular Genetics Lab, Department of Biological Science, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad 44000, Pakistan
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York 10032, USA
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York 10032, USA
| | | | - Suzanne M. Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, 10032 NY, USA
| | - Abdul Khaliq
- Human Molecular Genetics Lab, Department of Biological Science, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Asif Mir
- Human Molecular Genetics Lab, Department of Biological Science, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York 10032, USA
| |
Collapse
|
23
|
Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res 2022; 82:3888-3902. [PMID: 36251389 PMCID: PMC9627125 DOI: 10.1158/0008-5472.can-22-1123] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 07/29/2022] [Indexed: 02/03/2023]
Abstract
Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
Collapse
Affiliation(s)
- Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI
- William S. Middleton Memorial Veterans' Hospital, Madison, WI
| | | | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Corinne Maurice-Dror
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver, BC, Canada
| | - Ashutosh Maheshwari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wenbin Ye
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Jessica Petricca
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Marc D Perry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - William S Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Alicia K Morgans
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Robert E Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
| | - Matthew B Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Anders Bjartell
- Department of Translational Medicine, Medical Faculty, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin-Madison, Madison, WI
| | | | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
- Department of Urologic Surgery, University of California Davis, Sacramento, CA
| | - Phuoc T Tran
- Department of Radiation Oncology, University of Maryland, College Park, Baltimore, MD
| | - Edwin M Posadas
- Urologic Oncology Program & Uro-Oncology Research Laboratories, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Arc Institute, Palo Alto, CA
| | - Christopher A Maher
- Siteman Cancer Center, Washington University, St. Louis, MO
- McDonnell Genome Institute, Washington University, St. Louis, MO
- Department of Internal Medicine, Washington University, St. Louis, MO
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, Departments of Human Genetics and Urology, University of California Los Angeles, Los Angeles, CA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
| |
Collapse
|
24
|
Study of Single Nucleotide Polymorphisms Associated with Breast Cancer Patients among Arab Ancestries. Int J Breast Cancer 2022; 2022:2442109. [PMID: 36268271 PMCID: PMC9578870 DOI: 10.1155/2022/2442109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/20/2022] [Accepted: 09/30/2022] [Indexed: 11/27/2022] Open
Abstract
The aim of this study is to investigate the single nucleotide polymorphisms (SNPs) associated with breast cancer in our population of Arab patients. We investigated 26 breast cancer patients and an equal number of healthy age- and sex-matched control volunteers. We examined the exome wide microarray-based biomarkers and screened 243,345 SNPs for their possible significant association with our breast cancer patients. Successfully, we identified the most significant (p value ≤9.14 × 10−09) four associated SNPs [SNRK and SNRK-AS1-rs202018563G; BRCA2-rs2227943C; ZNF484-rs199826847C; and DCPS-rs1695739G] among persons with breast cancer versus the healthy controls even after Bonferroni corrections (p value <2.05 × 10−07). Although our patients' numbers were limited, the identified SNPs might shed some light on certain breast cancer-associated functional multigenic variations in Arab patients. We assert on the importance of more extensive large-scale analysis to confirm the candidate biomarkers and possible target genes of breast cancer among Arab ancestries.
Collapse
|
25
|
Hasin N, Riggs LM, Shekhtman T, Ashworth J, Lease R, Oshone RT, Humphries EM, Badner JA, Thomson PA, Glahn DC, Craig DW, Edenberg HJ, Gershon ES, McMahon FJ, Nurnberger JI, Zandi PP, Kelsoe JR, Roach JC, Gould TD, Ament SA. Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder. Mol Psychiatry 2022; 27:3842-3856. [PMID: 35546635 DOI: 10.1038/s41380-022-01609-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023]
Abstract
Bipolar disorder is an often-severe mental health condition characterized by alternation between extreme mood states of mania and depression. Despite strong heritability and the recent identification of 64 common variant risk loci of small effect, pathophysiological mechanisms remain unknown. Here, we analyzed genome sequences from 41 multiply-affected pedigrees and identified variants in 741 genes with nominally significant linkage or association with bipolar disorder. These 741 genes overlapped known risk genes for neurodevelopmental disorders and clustered within gene networks enriched for synaptic and nuclear functions. The top variant in this analysis - prioritized by statistical association, predicted deleteriousness, and network centrality - was a missense variant in the gene encoding D-amino acid oxidase (DAOG131V). Heterologous expression of DAOG131V in human cells resulted in decreased DAO protein abundance and enzymatic activity. In a knock-in mouse model of DAOG131, DaoG130V/+, we similarly found decreased DAO protein abundance in hindbrain regions, as well as enhanced stress susceptibility and blunted behavioral responses to pharmacological inhibition of N-methyl-D-aspartate receptors (NMDARs). RNA sequencing of cerebellar tissue revealed that DaoG130V resulted in decreased expression of two gene networks that are enriched for synaptic functions and for genes expressed, respectively, in Purkinje neurons or granule neurons. These gene networks were also down-regulated in the cerebellum of patients with bipolar disorder compared to healthy controls and were enriched for additional rare variants associated with bipolar disorder risk. These findings implicate dysregulation of NMDAR signaling and of gene expression in cerebellar neurons in bipolar disorder pathophysiology and provide insight into its genetic architecture.
Collapse
Affiliation(s)
- Naushaba Hasin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lace M Riggs
- Program in Neuroscience and Training Program in Integrative Membrane Biology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Robert Lease
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rediet T Oshone
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elizabeth M Humphries
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Judith A Badner
- Department of Psychiatry, Rush University Medical College, Chicago, IL, USA
| | - Pippa A Thomson
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland, UK
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | - Howard J Edenberg
- Departments of Biochemistry and Molecular Biology and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Elliot S Gershon
- Departments of Psychiatry and Human Genetics, University of Chicago, Chicago, IL, USA
| | - Francis J McMahon
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John R Kelsoe
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Todd D Gould
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
- Departments of Pharmacology and Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Veterans Affairs Maryland Health Care System, Baltimore, MD, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
26
|
Cole YC, Zhang YZ, Gallo B, Januszewski AP, Nastase A, Essex DJ, Thaung CMH, Cohen VML, Sagoo MS, Bowcock AM. Correlation between BAP1 Localization, Driver Mutations, and Patient Survival in Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14174105. [PMID: 36077643 PMCID: PMC9454448 DOI: 10.3390/cancers14174105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 12/02/2022] Open
Abstract
Uveal melanoma (UM) is an uncommon but highly aggressive ocular malignancy. Poor overall survival is associated with deleterious BAP1 alterations, which frequently occur with monosomy 3 (LOH3) and a characteristic gene expression profile. Tumor DNA from a cohort of 100 UM patients from Moorfields Biobank (UK) that had undergone enucleation were sequenced for known UM driver genes (BAP1, SF3B1, EIF1AX, GNAQ, and GNA11). Immunohistochemical staining of BAP1 and interphase FISH for chromosomes 3 and 8 was performed, and cellular localization of BAP1 was correlated with BAP1 mutations. Wildtype (WT) BAP1 staining was characterized by nBAP1 expression with <10% cytoplasmic BAP1 (cBAP1). Tumors exhibited heterogeneity with respect to BAP1 staining with different percentages of nBAP1 loss: ≥25% loss of nuclear BAP1 (nBAP1) was superior to chr8q and LOH3 as a prognostic indicator. Of the successfully sequenced UMs, 38% harbored oncogenic mutations in GNA11 and 48% harbored mutations in GNAQ at residues 209 or 183. Of the secondary drivers, 39% of mutations were in BAP1, 11% were in EIF1AX, and 20% were in the SF3B1 R625 hotspot. Most tumors with SF3B1 or EIF1AX mutations retained nuclear BAP1 (nBAP1). The majority of tumor samples with likely pathogenic BAP1 mutations, regardless of mutation class, displayed ≥25% loss of nBAP1. This included all tumors with truncating mutations and 80% of tumors with missense mutations. In addition, 60% of tumors with truncating mutations and 82% of tumors with missense mutations expressed >10% cBAP1.
Collapse
Affiliation(s)
- Yasemin C. Cole
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Yu-Zhi Zhang
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, UK
| | - Beatrice Gallo
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
| | - Adam P. Januszewski
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Anca Nastase
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - David J. Essex
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
| | - Caroline M. H. Thaung
- Moorfields Eye Hospital, London EC1V 2PD, UK
- Department of Eye Pathology, UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Victoria M. L. Cohen
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Mandeep S. Sagoo
- Ocular Oncology Service, Moorfields Eye Hospital & St. Bartholomew’s Hospital, London EC1V 2PD, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anne M. Bowcock
- National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
- Departments of Oncological Sciences, Dermatology and Genetics & Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: ; Tel.: +1-212-659-8256
| |
Collapse
|
27
|
Li K, Luo T, Zhu Y, Huang Y, Wang A, Zhang D, Dong L, Wang Y, Wang R, Tang D, Yu Z, Shen Q, Lv M, Ling Z, Fang Z, Yuan J, Li B, Xia K, He X, Li J, Zhao G. Performance evaluation of differential splicing analysis methods and splicing analytics platform construction. Nucleic Acids Res 2022; 50:9115-9126. [PMID: 35993808 PMCID: PMC9458456 DOI: 10.1093/nar/gkac686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/01/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
A proportion of previously defined benign variants or variants of uncertain significance in humans, which are challenging to identify, may induce an abnormal splicing process. An increasing number of methods have been developed to predict splicing variants, but their performance has not been completely evaluated using independent benchmarks. Here, we manually sourced ∼50 000 positive/negative splicing variants from > 8000 studies and selected the independent splicing variants to evaluate the performance of prediction methods. These methods showed different performances in recognizing splicing variants in donor and acceptor regions, reminiscent of different weight coefficient applications to predict novel splicing variants. Of these methods, 66.67% exhibited higher specificities than sensitivities, suggesting that more moderate cut-off values are necessary to distinguish splicing variants. Moreover, the high correlation and consistent prediction ratio validated the feasibility of integration of the splicing prediction method in identifying splicing variants. We developed a splicing analytics platform called SPCards, which curates splicing variants from publications and predicts splicing scores of variants in genomes. SPCards also offers variant-level and gene-level annotation information, including allele frequency, non-synonymous prediction and comprehensive functional information. SPCards is suitable for high-throughput genetic identification of splicing variants, particularly those located in non-canonical splicing regions.
Collapse
Affiliation(s)
| | | | - Yan Zhu
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuanfeng Huang
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - An Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Di Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Lijie Dong
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yujian Wang
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Dongdong Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhen Yu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Qunshan Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Mingrong Lv
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Zhengbao Ling
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jing Yuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei 230032, Anhui, China,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Bin Li
- Bioinformatics Center & National Clinical Research Centre for Geriatric Disorders & Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaojin He
- Correspondence may also be addressed to Xiaojin He. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| | - Jinchen Li
- To whom correspondence should be addressed. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| | - Guihu Zhao
- Correspondence may also be addressed to Guihu Zhao. Tel: +86 731 8975 2406; Fax: +86 731 8432 7332;
| |
Collapse
|
28
|
Aggregated Genomic Data as Cohort-Specific Allelic Frequencies can Boost Variants and Genes Prioritization in Non-Solved Cases of Inherited Retinal Dystrophies. Int J Mol Sci 2022; 23:ijms23158431. [PMID: 35955564 PMCID: PMC9368980 DOI: 10.3390/ijms23158431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
The introduction of NGS in genetic diagnosis has increased the repertoire of variants and genes involved and the amount of genomic information produced. We built an allelic-frequency (AF) database for a heterogeneous cohort of genetic diseases to explore the aggregated genomic information and boost diagnosis in inherited retinal dystrophies (IRD). We retrospectively selected 5683 index-cases with clinical exome sequencing tests available, 1766 with IRD and the rest with diverse genetic diseases. We calculated a subcohort’s IRD-specific AF and compared it with suitable pseudocontrols. For non-solved IRD cases, we prioritized variants with a significant increment of frequencies, with eight variants that may help to explain the phenotype, and 10/11 of uncertain significance that were reclassified as probably pathogenic according to ACMG. Moreover, we developed a method to highlight genes with more frequent pathogenic variants in IRD cases than in pseudocontrols weighted by the increment of benign variants in the same comparison. We identified 18 genes for further studies that provided new insights in five cases. This resource can also help one to calculate the carrier frequency in IRD genes. A cohort-specific AF database assists with variants and genes prioritization and operates as an engine that provides a new hypothesis in non-solved cases, augmenting the diagnosis rate.
Collapse
|
29
|
Deep Molecular Characterization of Milder Spinal Muscular Atrophy Patients Carrying the c.859G>C Variant in SMN2. Int J Mol Sci 2022; 23:ijms23158289. [PMID: 35955418 PMCID: PMC9368089 DOI: 10.3390/ijms23158289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 02/01/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a severe neuromuscular disorder caused by biallelic loss or pathogenic variants in the SMN1 gene. Copy number and modifier intragenic variants in SMN2, an almost identical paralog gene of SMN1, are known to influence the amount of complete SMN proteins. Therefore, SMN2 is considered the main phenotypic modifier of SMA, although genotype−phenotype correlation is not absolute. We present eleven unrelated SMA patients with milder phenotypes carrying the c.859G>C-positive modifier variant in SMN2. All were studied by a specific NGS method to allow a deep characterization of the entire SMN region. Analysis of two homozygous cases for the variant allowed us to identify a specific haplotype, Smn2-859C.1, in association with c.859G>C. Two other cases with the c.859G>C variant in their two SMN2 copies showed a second haplotype, Smn2-859C.2, in cis with Smn2-859C.1, assembling a more complex allele. We also identified a previously unreported variant in intron 2a exclusively linked to the Smn2-859C.1 haplotype (c.154-1141G>A), further suggesting that this region has been ancestrally conserved. The deep molecular characterization of SMN2 in our cohort highlights the importance of testing c.859G>C, as well as accurately assessing the SMN2 region in SMA patients to gain insight into the complex genotype−phenotype correlations and improve prognostic outcomes.
Collapse
|
30
|
Lee S, Jang S, Kim JI, Chae JH, Kim KJ, Lim BC. Whole genomic approach in mutation discovery of infantile spasms patients. Front Neurol 2022; 13:944905. [PMID: 35937050 PMCID: PMC9354570 DOI: 10.3389/fneur.2022.944905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022] Open
Abstract
Infantile spasms (IS) are a clinically and genetically heterogeneous group of epilepsy disorders in early infancy. The genetic backgrounds of IS have been gradually unraveled along with the increased application of next-generation sequencing (NGS). However, to date, only selected genomic regions have been sequenced using a targeted approach in most cases of IS, and the genetic etiologies of the majority of patients remain unknown. We conducted a proof-of-concept study using whole-genome sequencing (WGS) for the genetic diagnosis of IS. We included 16 patients with IS for this study, and WGS was applied as a first-tier test for genetic diagnosis. In total, we sequenced the whole genomes of 28 participants, including the genomes of six patients, which were sequenced with those of their parents. Among variants identified, we focused on those located in epilepsy or seizure-associated genes. We used two different methods to call relevant large deletions from WGS results. We found pathogenic or likely pathogenic variants in four patients (25.0%); a de novo variant in HDAC4, compound heterozygous variants in GRM7, and heterozygous variants in CACNA1E and KMT2E. We also selected two more candidate variants in SOX5 and SHROOM4 intronic regions. Although there are currently several difficulties in applying WGS for genetic diagnosis, especially in clinical interpretation of non-coding variants, we believe that developing sequencing technologies would overcome these hurdles in the near future. Considering the vast genetic heterogeneity and the substantial portion of patients with unknown etiologies, further studies using whole genomic approaches are necessary for patients with IS.
Collapse
Affiliation(s)
- Seungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Sesong Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Medical Research Center, Genomic Medicine Institute (GMI), Seoul National University, Seoul, South Korea
| | - Jong Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, South Korea
- *Correspondence: Byung Chan Lim
| |
Collapse
|
31
|
Berry V, Fujinami K, Mochizuki K, Iwata T, Pontikos N, Quinlan RA, Michaelides M. A recurrent variant in LIM2 causes an isolated congenital sutural/lamellar cataract in a Japanese family. Ophthalmic Genet 2022; 43:622-626. [PMID: 35736209 PMCID: PMC9612932 DOI: 10.1080/13816810.2022.2090010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Genetically determined cataract is both clinically and molecularly highly heterogeneous. Here, we have identified a heterozygous variant in the lens integral membrane protein LIM2, the second most abundant protein in the lens, responsible for congenital sutural/lamellar cataract in a three-generation Japanese family. Methods Whole exome sequencing (WES) was undertaken in one affected and one unaffected individual from a family with autosomal dominant congenital cataract to establish the underlying genetic basis. Results A recurrent missense variant LIM2: c.388C>T; p.R130C was identified and found to co-segregate with disease. In addition, one variant COL11A1:c.3788C>T of unknown significance (VUS) was also identified. Conclusions We report a variant in LIM2 causing an isolated autosomal-dominant congenital sutural/lamellar cataract in a Japanese family. This is the first report of a LIM2 variant in the Japanese population. Hence, we expand the mutation spectrum of LIM2 variants in different ethnic groups.
Collapse
Affiliation(s)
- Vanita Berry
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Kaoru Fujinami
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization, Tokyo Medical Centre, Tokyo, Japan
| | - Kiyofumi Mochizuki
- Department of Ophthalmology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Nikolas Pontikos
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Roy A Quinlan
- Department of Biosciences, University of Durham, Durham, UK
| | - Michel Michaelides
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| |
Collapse
|
32
|
Xu X, Jin K, Bais AS, Zhu W, Yagi H, Feinstein TN, Nguyen PK, Criscione JD, Liu X, Beutner G, Karunakaran KB, Rao KS, He H, Adams P, Kuo CK, Kostka D, Pryhuber GS, Shiva S, Ganapathiraju MK, Porter GA, Lin JHI, Aronow B, Lo CW. Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease. Cell Stem Cell 2022; 29:840-855.e7. [PMID: 35395180 PMCID: PMC9302582 DOI: 10.1016/j.stem.2022.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/19/2021] [Accepted: 03/08/2022] [Indexed: 12/14/2022]
Abstract
Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease with 30% mortality from heart failure (HF) in the first year of life, but the cause of early HF remains unknown. Induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CM) from patients with HLHS showed that early HF is associated with increased apoptosis, mitochondrial respiration defects, and redox stress from abnormal mitochondrial permeability transition pore (mPTP) opening and failed antioxidant response. In contrast, iPSC-CM from patients without early HF showed normal respiration with elevated antioxidant response. Single-cell transcriptomics confirmed that early HF is associated with mitochondrial dysfunction accompanied with endoplasmic reticulum (ER) stress. These findings indicate that uncompensated oxidative stress underlies early HF in HLHS. Importantly, mitochondrial respiration defects, oxidative stress, and apoptosis were rescued by treatment with sildenafil to inhibit mPTP opening or TUDCA to suppress ER stress. Together these findings point to the potential use of patient iPSC-CM for modeling clinical heart failure and the development of therapeutics.
Collapse
Affiliation(s)
- Xinxiu Xu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
| | - Abha S Bais
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wenjuan Zhu
- Centre for Cardiovascular Genomics and Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Hisato Yagi
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy N Feinstein
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Phong K Nguyen
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Joseph D Criscione
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Xiaoqin Liu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gisela Beutner
- Departments of Pediatrics and Environmental Medicine University of Rochester Medical Center Rochester, NY USA
| | - Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
| | - Krithika S Rao
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haoting He
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Phillip Adams
- Anesthesiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Catherine K Kuo
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA; Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Computational & Systems Biology and Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gloria S Pryhuber
- Departments of Pediatrics and Environmental Medicine University of Rochester Medical Center Rochester, NY USA
| | - Sruti Shiva
- Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - George A Porter
- Pediatrics, Pharmacology, and Physiology, Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Jiuann-Huey Ivy Lin
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45256, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
33
|
Takai E, Nakamura H, Chiku S, Kubo E, Ohmoto A, Totoki Y, Shibata T, Higuchi R, Yamamoto M, Furuse J, Shimizu K, Takahashi H, Morizane C, Furukawa T, Yachida S. Whole-exome Sequencing Reveals New Potential Susceptibility Genes for Japanese Familial Pancreatic Cancer. Ann Surg 2022; 275:e652-e658. [PMID: 32826389 DOI: 10.1097/sla.0000000000004213] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The primary objective of this study was to identify novel genes that predispose people in the Japanese population to FPC. SUMMARY OF BACKGROUND DATA Familial history of pancreatic cancer is an important risk factor but, to date, few genes predisposing individuals to increased risk of developing FPC have been identified. METHODS We performed whole-exome sequencing of germline DNA from 81 Japanese FPC patients. We also investigated somatic gene alterations in 21 matched tumor tissues through whole-exome sequencing and copy number analysis. RESULTS Our germline variants identified previously known FPC susceptibility genes such as ATM and BRCA2, and several novel tumor suppressor genes with potentially deleterious variants for FPC. Interestingly, somatic whole-exome analysis demonstrated that most tumor samples with suspicious loss of heterozygosity of candidate genes were KRAS wild-types, implying that these cases may not have required KRAS activation as a driver event for carcinogenesis. CONCLUSIONS Our findings indicate that FPC patients harbor potentially deleterious causative germline variants in tumor suppressor genes, which are known to acquire somatic mutations in pancreatic cancer, and that somatic loss of heterozygosity of some FPC susceptibility genes may contribute to the development of FPC in the absence of somatic KRAS-activating mutation. Genetic testing for a wider variety of FPC-predisposition genes could provide better screening approach for high-risk groups of pancreatic cancer.
Collapse
Affiliation(s)
- Erina Takai
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Suenori Chiku
- Information and Communication Research Division, Mizuho Information and Research Institute, Tokyo, Japan
| | - Emi Kubo
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Akihiro Ohmoto
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Ryota Higuchi
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Masakazu Yamamoto
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Junji Furuse
- Department of Medical Oncology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Kyoko Shimizu
- Department of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Hideaki Takahashi
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Chigusa Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Toru Furukawa
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| |
Collapse
|
34
|
Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift. Genes (Basel) 2022; 13:genes13040569. [PMID: 35456375 PMCID: PMC9028680 DOI: 10.3390/genes13040569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Most genetic variants are rare and specific to the population, highlighting the importance of characterizing local population genetic diversity. Many countries have initiated population-based whole-genome sequencing (WGS) studies. Genomic variation within Lithuanian families are not available in the public databases. Here, we describe initial findings of a high-coverage (an average of 36.27×) whole genome sequencing for 25 trios of the Lithuanian population. Each genome on average carried approximately 4,701,473 (±28,255) variants, where 80.6% (3,787,626) were single nucleotide polymorphisms (SNPs), and the rest 19.4% were indels. An average of 12.45% was novel according to dbSNP (build 150). The WGS structural variation (SV) analysis identified on average 9133 (±85.10) SVs, of which 95.85% were novel. De novo single nucleotide variation (SNV) analysis identified 4417 variants, where 1.1% de novo SNVs were exonic, 43.9% intronic, 51.9% intergenic, and the rest 3.13% in UTR or downstream sequence. Three potential pathogenic de novo variants in the ZSWIM8, CDC42EP1, and RELA genes were identified. Our findings provide useful information on local human population genomic variation, especially for de novo variants, and will be a valuable resource for further genetic studies, and medical implications.
Collapse
|
35
|
Almandil NB, AlSulaiman A, Aldakeel SA, Alkuroud DN, Aljofi HE, Alzahrani S, Al-mana A, Alfuraih AA, Alabdali M, Alkhamis FA, AbdulAzeez S, Borgio JF. Integration of Transcriptome and Exome Genotyping Identifies Significant Variants with Autism Spectrum Disorder. Pharmaceuticals (Basel) 2022; 15:ph15020158. [PMID: 35215271 PMCID: PMC8880056 DOI: 10.3390/ph15020158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
Autism is a complex disease with genetic predisposition factors. Real factors for treatment and early diagnosis are yet to be defined. This study integrated transcriptome and exome genotyping for identifying functional variants associated with autism spectrum disorder and their impact on gene expression to find significant variations. More than 1800 patients were screened, and 70 (47 male/23 female) with an average age of 7.56 ± 3.68 years fulfilled the DSM-5 criteria for autism. Analysis revealed 682 SNPs of 589 genes significantly (p < 0.001) associated with autism among the putative functional exonic variants (n = 243,345) studied. Olfactory receptor genes on chromosome 6 were significant after Bonferroni correction (α = 0.05/243345 = 2.05 × 10−7) with a high degree of linkage disequilibrium on 6p22.1 (p = 6.71 × 10−9). The differentially expressed gene analysis of autistic patients compared to controls in whole RNA sequencing identified significantly upregulated (foldchange ≥ 0.8 and p-value ≤ 0.05; n = 125) and downregulated (foldchange ≤ −0.8 and p-value ≤ 0.05; n = 117) genes. The integration of significantly up- and downregulated genes and genes of significant SNPs identified regulatory variants (rs6657480, rs3130780, and rs1940475) associated with the up- (ITGB3BP) and downregulation (DDR1 and MMP8) of genes in autism spectrum disorder in people of Arab ancestries. The significant variants could be a biomarker of interest for identifying early autism among Arabs and helping to characterize the genes involved in the susceptibility mechanisms for autistic subjects.
Collapse
Affiliation(s)
- Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Abdulla AlSulaiman
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Sumayh A. Aldakeel
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Deem N. Alkuroud
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Halah Egal Aljofi
- Environmental Health Research Area, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Safah Alzahrani
- Department of Mental Health, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.); (A.A.-m.)
- King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Aishah Al-mana
- Department of Mental Health, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.); (A.A.-m.)
- King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Asma A. Alfuraih
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Majed Alabdali
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Fahd A. Alkhamis
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
- Correspondence: ; Tel.: +966-13-3330864
| |
Collapse
|
36
|
Computational Resources for the Interpretation of Variations in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:177-198. [DOI: 10.1007/978-3-030-91836-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
37
|
Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. Genes (Basel) 2021; 13:genes13010087. [PMID: 35052430 PMCID: PMC8774935 DOI: 10.3390/genes13010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
Conventional genome-wide association studies (GWASs) of complex traits, such as Multiple Sclerosis (MS), are reliant on per-SNP p-values and are therefore heavily burdened by multiple testing correction. Thus, in order to detect more subtle alterations, ever increasing sample sizes are required, while ignoring potentially valuable information that is readily available in existing datasets. To overcome this, we used penalised regression incorporating elastic net with a stability selection method by iterative subsampling to detect the potential interaction of loci with MS risk. Through re-analysis of the ANZgene dataset (1617 cases and 1988 controls) and an IMSGC dataset as a replication cohort (1313 cases and 1458 controls), we identified new association signals for MS predisposition, including SNPs above and below conventional significance thresholds while targeting two natural killer receptor loci and the well-established HLA loci. For example, rs2844482 (98.1% iterations), otherwise ignored by conventional statistics (p = 0.673) in the same dataset, was independently strongly associated with MS in another GWAS that required more than 40 times the number of cases (~45 K). Further comparison of our hits to those present in a large-scale meta-analysis, confirmed that the majority of SNPs identified by the elastic net model reached conventional statistical GWAS thresholds (p < 5 × 10−8) in this much larger dataset. Moreover, we found that gene variants involved in oxidative stress, in addition to innate immunity, were associated with MS. Overall, this study highlights the benefit of using more advanced statistical methods to (re-)analyse subtle genetic variation among loci that have a biological basis for their contribution to disease risk.
Collapse
|
38
|
Zanette V, Valle DD, Telles BA, Robinson AJ, Monteiro V, Santos MLSF, Souza RLR, Benincá C. NDUFV1 mutations in complex I deficiency: Case reports and review of symptoms. Genet Mol Biol 2021; 44:e20210149. [PMID: 34807224 PMCID: PMC8607527 DOI: 10.1590/1678-4685-gmb-2021-0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/18/2021] [Indexed: 11/22/2022] Open
Abstract
Mitochondrial complex I (CI) deficiency is the most common oxidative phosphorylation disorder described. It shows a wide range of phenotypes with poor correlation within genotypes. Herein we expand the clinics and genetics of CI deficiency in the brazilian population by reporting three patients with pathogenic (c.640G>A, c.1268C>T, c.1207dupG) and likely pathogenic (c.766C>T) variants in the NDUFV1 gene. We show the mutation c.766C>T associated with a childhood onset phenotype of hypotonia, muscle weakness, psychomotor regression, lethargy, dysphagia, and strabismus. Additionally, this mutation was found to be associated with headaches and exercise intolerance in adulthood. We also review reported pathogenic variants in NDUFV1 highlighting the wide phenotypic heterogeneity in CI deficiency.
Collapse
Affiliation(s)
- Vanessa Zanette
- Universidade Federal do Paraná, Departamento de Genética, Laboratório de Polimorfismos e Ligação, Curitiba, PR, Brazil
| | - Daniel do Valle
- Hospital Pequeno Príncipe, Divisão de Neuropediatria, Curitiba, PR, Brazil
| | | | - Alan J Robinson
- University of Cambridge, Medical Research Council, Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - Vaneisse Monteiro
- Hospital Pequeno Príncipe, Divisão de Neuropediatria, Curitiba, PR, Brazil
| | | | - Ricardo Lehtonen R Souza
- Universidade Federal do Paraná, Departamento de Genética, Laboratório de Polimorfismos e Ligação, Curitiba, PR, Brazil
| | - Cristiane Benincá
- Universidade Federal do Paraná, Departamento de Genética, Laboratório de Polimorfismos e Ligação, Curitiba, PR, Brazil.,University of Cambridge, Medical Research Council, Mitochondrial Biology Unit, Cambridge, United Kingdom
| |
Collapse
|
39
|
Patel CK, Broadgate S, Shalaby A, Yu J, Nemeth AH, Downes SM, Halford S. Whole genome sequencing in a Knobloch syndrome family confirms the molecular diagnosis. Ophthalmic Genet 2021; 43:201-209. [PMID: 34751625 DOI: 10.1080/13816810.2021.1998554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND To establish the molecular diagnosis in two brothers presenting with the ocular features of Knobloch Syndrome using whole genome sequencing (WGS). METHODS Clinical examination and ophthalmological phenotyping were completed under general anaesthesia. DNA samples were tested on a targeted retinal dystrophy next-generation sequencing panel. Subsequently, WGS was performed to identify additional variants. RESULTS Clinical examination confirmed the diagnosis of Knobloch Syndrome. Targeted sequencing identified a novel heterozygous frameshift pathogenic variant in COL18A1, c.2864dupC; p.(Gly956ArgfsX20), inherited from their mother. A second paternally inherited heterozygous missense variant was identified in both brothers, c.5014 G > A; p.(Asp1672Asn), which was initially considered to have too high frequency to be pathogenic (MAF 8.8%). This led to an in-depth analysis of the COL18A1 locus using WGS data, which confirmed that Asp1672Asn is a likely pathogenic hypomorphic allele. CONCLUSION To date, all confirmed genetic diagnoses of Knobloch syndrome are attributable to variants in COL18A1. The family described here has a heterozygous novel loss of function variant. Detailed analysis of WGS data combined with family segregation studies concluded that although Asp1672Asn has a high population frequency, it is the most likely second pathogenic variant in our family. This supports the hypothesis that this is a hypomorphic allele, which, in combination with a loss of function pathogenic variant, leads to Knobloch syndrome.To our knowledge, this is the first time that WGS has been used to confirm a molecular diagnosis of Knobloch syndrome in this way and has provided further insight into the molecular mechanisms in this rare disorder.
Collapse
Affiliation(s)
| | - Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Ahmed Shalaby
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Andrea H Nemeth
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Centre for Genomic Medicine, Oxford, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| |
Collapse
|
40
|
Borgio JF, Alsuwat HS, Alamoudi W, Hegazi FM, Al Otaibi WM, M Ibrahim A, Almandil NB, Al-Amodi AM, Alyousef YM, AlShwaimi E, Almasoud N, Kamaraj B, Sayed A. Exome array identifies functional exonic biomarkers for pediatric dental caries. Comput Biol Med 2021; 141:105019. [PMID: 34749984 DOI: 10.1016/j.compbiomed.2021.105019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND Pediatric dental caries is common among Arab children, however we are still searching for possible genes and molecular mechanisms that influence caries development. AIM To identity genetic predispositions of dental caries among Saudi children with high DMFT (Decayed, Missing, and Filled Teeth). DESIGN This case-control study analysed putative functional exonic-variants (n = 243,345) to study the molecular genetics of pediatric caries with high dmft index, 8.75 ± 4.16 on Arab-ancestry subjects with primary dentition (n = 111; 76 cases, dmft>5 and 35 controls, dmft = 0). RESULTS Pediatric caries is significantly associated with single nucleotide polymorphisms (SNP) in the GRIN2B-rs4764039C (p-value = 2.03 × 10-08) and CFH-rs1065489G (p-value = 8.26 × 10-08) genes, even after Bonferroni correction. Irregular tooth brushing habits (p = 0.0404) and irregular dental visits (p = 0.0050) are significantly associated with caries. Functional enrichment analysis of significant genes is associated with calcium-activated chloride channel, Staphylococcus aureus infection, and N-linked glycosylation. CONCLUSION Genetic predispositions are found to be significantly associated with the high prevalence of pediatric caries, which is a disorder of multigene-environment interaction. The significant functional exonic variants identified can be biomarkers for the early diagnosis of pediatric dental caries in Arabs.
Collapse
Affiliation(s)
- J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Hind Saleh Alsuwat
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Widyan Alamoudi
- Departments of Neuroscience Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fatma Mohammed Hegazi
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Waad Mohammed Al Otaibi
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdallah M Ibrahim
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia; Department of Fundamentals of Nursing, College of Nursing, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Amani M Al-Amodi
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Yousef M Alyousef
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Emad AlShwaimi
- Department of Restorative Dental Science, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Naif Almasoud
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
| | - AbdulAzeez Sayed
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| |
Collapse
|
41
|
Petrazzini BO, Naya H, Lopez-Bello F, Vazquez G, Spangenberg L. Evaluation of different approaches for missing data imputation on features associated to genomic data. BioData Min 2021; 14:44. [PMID: 34479616 PMCID: PMC8414708 DOI: 10.1186/s13040-021-00274-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/08/2021] [Indexed: 12/12/2022] Open
Abstract
Background Missing data is a common issue in different fields, such as electronics, image processing, medical records and genomics. They can limit or even bias the posterior analysis. The data collection process can lead to different distribution, frequency, and structure of missing data points. They can be classified into four categories: Structurally Missing Data (SMD), Missing Completely At Random (MCAR), Missing At Random (MAR) and Missing Not At Random (MNAR). For the three later, and in the context of genomic data (especially non-coding data), we will discuss six imputation approaches using 31,245 variants collected from ClinVar and annotated with 13 genome-wide features. Results Random Forest and kNN algorithms showed the best performance in the evaluated dataset. Additionally, some features show robust imputation regardless of the algorithm (e.g. conservation scores phyloP7 and phyloP20), while other features show poor imputation across algorithms (e.g. PhasCons). We also developed an R package that helps to test which imputation method is the best for a particular data set. Conclusions We found that Random Forest and kNN are the best imputation method for genomics data, including non-coding variants. Since Random Forest is computationally more challenging, kNN remains a more realistic approach. Future work on variant prioritization thru genomic screening tests could largely profit from this methodology. Supplementary Information The online version contains supplementary material available at 10.1186/s13040-021-00274-7.
Collapse
Affiliation(s)
- Ben Omega Petrazzini
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hugo Naya
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.,Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, 12900, Montevideo, Uruguay
| | | | - Gustavo Vazquez
- Department of Informatics and Computer Science, Universidad Católica del Uruguay, Av. 8 de Octubre, 2738, 11600, Montevideo, Uruguay
| | - Lucía Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay. .,Department of Informatics and Computer Science, Universidad Católica del Uruguay, Av. 8 de Octubre, 2738, 11600, Montevideo, Uruguay.
| |
Collapse
|
42
|
Yu M, Kyryachenko S, Debette S, Amouyel P, Schott JJ, Le Tourneau T, Dina C, Norris RA, Hagège AA, Jeunemaitre X, Bouatia-Naji N. Genome-Wide Association Meta-Analysis Supports Genes Involved in Valve and Cardiac Development to Associate With Mitral Valve Prolapse. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003148. [PMID: 34461747 DOI: 10.1161/circgen.120.003148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mitral valve prolapse (MVP) is a common cardiac valve disease, which affects 1 in 40 in the general population. Previous genome-wide association study has identified 6 risk loci for MVP. But these loci explained only partially the genetic risk for MVP. We aim to identify additional risk loci for MVP by adding data set from the UK Biobank. METHODS We also incorporated 434 MVP cases and 4527 controls from the UK Biobank for discovery analyses. Genetic association was conducted using SNPTEST and meta-analyses using METAL. We used Functional Mapping and Annotation of Genome-Wide Association Studies for post-genome-wide association study annotations and Multi-marker Analysis of GenoMic Annotation for gene-based and gene-set analyses. RESULTS We found Trans-Omics for Precision Medicine imputation to perform better in terms of accuracy in the lower ranges of minor allele frequency below 0.1. Our updated meta-analysis included UK Biobank study for ≈8 million common single-nucleotide polymorphisms (minor allele frequency >0.01) and replicated the association on Chr2 as the top association signal near TNS1. We identified an additional risk locus on Chr1 (SYT2) and 2 suggestive risk loci on chr8 (MSRA) and chr19 (FBXO46), all driven by common variants. Gene-based association using Multi-marker Analysis of GenoMic Annotation revealed 6 risk genes for MVP with pronounced expression levels in cardiovascular tissues, especially the heart and globally part of enriched GO terms related to cardiac development. CONCLUSIONS We report an updated meta-analysis genome-wide association study for MVP using dense imputation coverage and an improved case-control sample. We describe several loci and genes with MVP spanning biological mechanisms highly relevant to MVP, especially during valve and heart development.
Collapse
Affiliation(s)
- Mengyao Yu
- PARCC, Inserm, Université de Paris, F-75015, Paris, France (M.Y., S.K., X.J., N.B.-N.)
| | - Sergiy Kyryachenko
- PARCC, Inserm, Université de Paris, F-75015, Paris, France (M.Y., S.K., X.J., N.B.-N.)
| | - Stephanie Debette
- Bordeaux Population Health Research Center, Inserm Center U1219, University of Bordeaux, France (S.D.).,Department of Neurology, Bordeaux University Hospital, Inserm U1219, France (S.D.)
| | - Philippe Amouyel
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Labex DISTALZ - Risk Factors and Molecular Determinants of Aging-Related Disease, Lille, France (P.A.)
| | - Jean-Jacques Schott
- Université de Nantes, INSERM, CNRS, CHU Nantes, l'institut du thorax, F-44000, France (J.-J.S., T.L.T., C.D.)
| | - Thierry Le Tourneau
- Université de Nantes, INSERM, CNRS, CHU Nantes, l'institut du thorax, F-44000, France (J.-J.S., T.L.T., C.D.)
| | - Christian Dina
- Université de Nantes, INSERM, CNRS, CHU Nantes, l'institut du thorax, F-44000, France (J.-J.S., T.L.T., C.D.)
| | - Russell A Norris
- Department of Regenerative Medicine and Cell Biology (R.A.N.), Medical University of South Carolina, Charleston, SC.,Department of Medicine (R.A.N.), Medical University of South Carolina, Charleston, SC
| | - Albert A Hagège
- Assistance Publique - Hôpitaux de Paris, Department of Cardiology, Hôpital Européen Georges Pompidou, France (A.A.H.)
| | - Xavier Jeunemaitre
- PARCC, Inserm, Université de Paris, F-75015, Paris, France (M.Y., S.K., X.J., N.B.-N.)
| | - Nabila Bouatia-Naji
- PARCC, Inserm, Université de Paris, F-75015, Paris, France (M.Y., S.K., X.J., N.B.-N.)
| |
Collapse
|
43
|
Compact RNA editors with small Cas13 proteins. Nat Biotechnol 2021; 40:194-197. [PMID: 34462587 DOI: 10.1038/s41587-021-01030-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/20/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas13 systems have been developed for precise RNA editing, and can potentially be used therapeutically when temporary changes are desirable or when DNA editing is challenging. We have identified and characterized an ultrasmall family of Cas13b proteins-Cas13bt-that can mediate mammalian transcript knockdown. We have engineered compact variants of REPAIR and RESCUE RNA editors by functionalizing Cas13bt with adenosine and cytosine deaminase domains, and demonstrated packaging of the editors within a single adeno-associated virus.
Collapse
|
44
|
Berry V, Ionides A, Pontikos N, Moore AT, Quinlan RA, Michaelides M. Variants in PAX6, PITX3 and HSF4 causing autosomal dominant congenital cataracts. Eye (Lond) 2021; 36:1694-1701. [PMID: 34345029 PMCID: PMC9307513 DOI: 10.1038/s41433-021-01711-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/09/2022] Open
Abstract
Background Lens development is orchestrated by transcription factors. Disease-causing variants in transcription factors and their developmental target genes are associated with congenital cataracts and other eye anomalies. Methods Using whole exome sequencing, we identified disease-causing variants in two large British families and one isolated case with autosomal dominant congenital cataract. Bioinformatics analysis confirmed these disease-causing mutations as rare or novel variants, with a moderate to damaging pathogenicity score, with testing for segregation within the families using direct Sanger sequencing. Results Family A had a missense variant (c.184 G>A; p.V62M) in PAX6 and affected individuals presented with nuclear cataract. Family B had a frameshift variant (c.470–477dup; p.A160R*) in PITX3 that was also associated with nuclear cataract. A recurrent missense variant in HSF4 (c.341 T>C; p.L114P) was associated with congenital cataract in a single isolated case. Conclusions We have therefore identified novel variants in PAX6 and PITX3 that cause autosomal dominant congenital cataract.
Collapse
Affiliation(s)
- Vanita Berry
- UCL Institute of Ophthalmology, University College London, London, UK. .,Moorfields Eye Hospital NHS Foundation Trust, London, UK.
| | - Alex Ionides
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Roy A Quinlan
- School of Biological and Medical Sciences, University of Durham, Durham, UK
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London, UK. .,Moorfields Eye Hospital NHS Foundation Trust, London, UK.
| |
Collapse
|
45
|
Novel STAG1 Frameshift Mutation in a Patient Affected by a Syndromic Form of Neurodevelopmental Disorder. Genes (Basel) 2021; 12:genes12081116. [PMID: 34440290 PMCID: PMC8392311 DOI: 10.3390/genes12081116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/24/2022] Open
Abstract
The cohesin complex is a large evolutionary conserved functional unit which plays an essential role in DNA repair and replication, chromosome segregation and gene expression. It consists of four core proteins, SMC1A, SMC3, RAD21, and STAG1/2, and by proteins regulating the interaction between the complex and the chromosomes. Mutations in the genes coding for these proteins have been demonstrated to cause multisystem developmental disorders known as “cohesinopathies”. The most frequent and well recognized among these distinctive clinical conditions are the Cornelia de Lange syndrome (CdLS, OMIM 122470) and Roberts syndrome (OMIM 268300). STAG1 belongs to the STAG subunit of the core cohesin complex, along with five other subunits. Pathogenic variants in STAG1 gene have recently been reported to cause an emerging syndromic form of neurodevelopmental disorder that is to date poorly characterized. Here, we describe a 5 year old female patient with neurodevelopmental delay, mild intellectual disability, dysmorphic features and congenital anomalies, in which next generation sequencing analysis allowed us to identify a novel pathogenic variation c.2769_2770del p.(Ile924Serfs*8) in STAG1 gene, which result to be de novo. The variant has never been reported before in medical literature and is absent in public databases. Thus, it is useful to expand the molecular spectrum of clinically relevant alterations of STAG1 and their phenotypic consequences.
Collapse
|
46
|
Rosenbaum JN, Berry AB, Church AJ, Crooks K, Gagan JR, López-Terrada D, Pfeifer JD, Rennert H, Schrijver I, Snow AN, Wu D, Ewalt MD. A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee. J Mol Diagn 2021; 23:1218-1240. [PMID: 34245921 DOI: 10.1016/j.jmoldx.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Molecular genetic pathology (MGP) is a subspecialty of pathology and medical genetics and genomics. Genomic testing, which we define as that which generates large data sets and interrogates large segments of the genome in a single assay, is increasingly recognized as essential for optimal patient care through precision medicine. The most common genomic testing technologies in clinical laboratories are next-generation sequencing and microarray. It is essential to train in these methods and to consider the data generated in the context of the diagnosis, medical history, and other clinical findings of individual patients. Accordingly, updating the MGP fellowship curriculum to include genomics is timely, important, and challenging. At the completion of training, an MGP fellow should be capable of independently interpreting and signing out results of a wide range of genomic assays and, given the appropriate context and institutional support, of developing and validating new assays in compliance with applicable regulations. The Genomics Task Force of the MGP Program Directors, a working group of the Association for Molecular Pathology Training and Education Committee, has developed a genomics curriculum framework and recommendations specific to the MGP fellowship. These recommendations are presented for consideration and implementation by MGP fellowship programs with the understanding that MGP programs exist in a diversity of clinical practice environments with a spectrum of available resources.
Collapse
Affiliation(s)
- Jason N Rosenbaum
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna B Berry
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Swedish Cancer Institute and Institute of Systems Biology, Seattle, Washington
| | - Alanna J Church
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Kristy Crooks
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jeffrey R Gagan
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Dolores López-Terrada
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Baylor College of Medicine, Houston, Texas
| | - John D Pfeifer
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Hanna Rennert
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Iris Schrijver
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anthony N Snow
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - David Wu
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Mark D Ewalt
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
47
|
Osman Y, Elsharkawy T, Hashim TM, Alratroot JA, Alsuwat HS, Otaibi WMA, Hegazi FM, AbdulAzeez S, Borgio JF. Functional multigenic variations associated with hodgkin lymphoma. Int J Lab Hematol 2021; 43:1472-1482. [PMID: 34216518 DOI: 10.1111/ijlh.13644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The current study aimed to describe genotypes associated with Hodgkin lymphoma (HL) in a cohort of Saudi and non-Saudi patients and discuss their possible susceptibility to HL. METHODS We studied clinical, histopathological, and laboratory findings of HL patients admitted over 12 years duration, at King Fahd University Hospital, KSA. The genomic DNAs of HL patients (n = 61) and normal control subjects (n = 36) were extracted, and genotyping was performed using the Illumina human exome bead chip. Set of HL patients and set of normal controls were included in this study. RESULTS A total of 35 DNA variants were found to be highly significant with the P-value <9.90 × 10-11 among 243 345 exonic biomarkers and obeying the Hardy-Weinberg equilibrium. Nine, MEGF11-rs150945752 (P-value 1.20 × 10-12 ), CACNA1I- s58055559 (P-value 1.93 × 10-12 ), DECR2-rs146760080 (P-value 2.19 × 10-12 ), STAB1-rs143894786 (P-value 2.45 × 10-12 ), ZNF526-rs144433879 (P-value 2.76 × 10-12 ), CPLANE1-rs200612080 (P-value 3.77 × 10-12 ), DLK1-rs1058009 (P-value 5.95 × 10-12 ), RTN4RL2-rs61745214 (P-value 7.71 × 10-12 ), and PGRMC1-rs145582672 (P-value 8.56 × 10-12 ), exonic variants on chromosomes 15, 22, and 16 were highly associated with HL cases. THE HIGHLY SIGNIFICANT HAPLOTYPES AT CHROMOSOME 3: rs143894786G; rs149982219G with P-value = 3.43 × 10-14 was found to be the risk haplotype for the HL patients. The opposite alleles at chromosome 3: rs143894786A; rs149982219G is protective with P-value = 2.46 × 10-12 . Maximum number of SNPs at the chromosome 19: rs144433879C; rs181265966G; rs201144421C; rs145591797G; rs200560875G; rs77270337G (risk P-value = 2.24 × 10-12 ) and its opposite allele rs144433879A; rs181265966A; rs201144421T; rs145591797A; rs200560875A; rs77270337A (protective P-value = 2.60 × 10-9 ) were found to be associated haplotype with the HL and controls, respectively, in Saudi population. CONCLUSION Our study concludes that the HL is genetically heterogeneous with multigene causation.
Collapse
Affiliation(s)
- Yasser Osman
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Tarek Elsharkawy
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Tariq Mohammad Hashim
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Hind Saleh Alsuwat
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Waad Mohammed Al Otaibi
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fatma Mohammed Hegazi
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| |
Collapse
|
48
|
Khodakov D, Li J, Zhang JX, Zhang DY. Highly multiplexed rapid DNA detection with single-nucleotide specificity via convective PCR in a portable device. Nat Biomed Eng 2021; 5:702-712. [PMID: 34211146 DOI: 10.1038/s41551-021-00755-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/24/2021] [Indexed: 02/02/2023]
Abstract
Assays for the molecular detection of nucleic acids are typically constrained by the level of multiplexing (this is the case for the quantitative polymerase chain reaction (qPCR) and for isothermal amplification), turnaround times (as with microarrays and next-generation sequencing), quantification accuracy (isothermal amplification, microarrays and nanopore sequencing) or specificity for single-nucleotide differences (microarrays and nanopore sequencing). Here we show that a portable and battery-powered PCR assay performed in a toroidal convection chamber housing a microarray of fluorescently quenched oligonucleotide probes allows for the rapid and sensitive quantification of multiple DNA targets with single-nucleotide discrimination. The assay offers a limit of detection of 10 DNA copies within 30 min of turnaround time and a dynamic range spanning 4 orders of magnitude of DNA concentration, and we show its performance by detecting 20 genomic loci and 30 single-nucleotide polymorphisms in human genomic DNA samples, and 15 bacterial species in clinical isolates. Portable devices for the fast and highly multiplexed detection of nucleic acids may offer advantages in point-of-care diagnostics.
Collapse
Affiliation(s)
- Dmitriy Khodakov
- Department of Bioengineering, Rice University, Houston, TX, USA.,Torus Biosystems, Cambridge, MA, USA
| | - Jiaming Li
- Department of Bioengineering, Rice University, Houston, TX, USA.,Department of Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Jinny X Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA.,Department of Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.,Nuprobe USA, Houston, TX, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA. .,Department of Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.
| |
Collapse
|
49
|
Shen L, McCormick EM, Muraresku CC, Falk MJ, Gai X. Clinical Bioinformatics in Precise Diagnosis of Mitochondrial Disease. Clin Lab Med 2021; 40:149-161. [PMID: 32439066 DOI: 10.1016/j.cll.2020.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Clinical bioinformatics system is well-established for diagnosing genetic disease based on next-generation sequencing, but requires special considerations when being adapted for the next-generation sequencing-based genetic diagnosis of mitochondrial diseases. Challenges are caused by the involvement of mitochondrial DNA genome in disease etiology. Heteroplasmy and haplogroup are key factors in interpreting mitochondrial DNA variant effects. Data resources and tools for analyzing variant and sequencing data are available at MSeqDR, MitoMap, and HmtDB. Revised specifications of the American College of Medical Genetics/Association of Molecular Pathology standards and guidelines for mitochondrial DNA variant interpretation are proposed by the MSeqDr Consortium and community experts.
Collapse
Affiliation(s)
- Lishuang Shen
- Keck School of Medicine of USC, Center for Personalized Medicine, Children's Hospital Los Angeles, Suite 300, 2100 West 3rd Street, Los Angeles, CA 90057, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Colleen Clarke Muraresku
- Mitochondrial Medicine Frontier Program, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Marni J Falk
- CHOP Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, The Children's Hospital of Philadelphia, ARC 1002c, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Xiaowu Gai
- Keck School of Medicine of USC, Center for Personalized Medicine, Children's Hospital Los Angeles, Suite 300, 2100 West 3rd Street, Los Angeles, CA 90057, USA.
| |
Collapse
|
50
|
Leone MP, Palumbo P, Saenen J, Mastroianno S, Castellana S, Amico C, Mazza T, Potenza DR, Petracca A, Castori M, Carella M, Di Stolfo G. Phenotypic Variability of a Pathogenic PKP2 Mutation in an Italian Family Affected by Arrhythmogenic Cardiomyopathy and Juvenile Sudden Death: Considerations From Molecular Autopsy to Sport Restriction. Front Cardiovasc Med 2021; 8:635141. [PMID: 34095246 PMCID: PMC8173114 DOI: 10.3389/fcvm.2021.635141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/01/2021] [Indexed: 01/11/2023] Open
Abstract
Background: Arrhythmogenic cardiomyopathy (ACM) is a genetic disorder with an estimated prevalence between 1:2,000 and 1:5,000 and is characterized by the fibrofatty replacement of cardiomyocytes that predisposes to malignant arrhythmias, heart failure, and sudden cardiac death. The diagnosis is based on the 2010 Task Force Criteria including family history, electrocardiographic traits and arrhythmogenic pattern, specific gene mutations, and structural and/or histological abnormalities. Most ACMs display an autosomal dominant mode of inheritance often with incomplete penetrance and variable expressivity. Genetic screening of patients with ACM identifies pathogenic or likely pathogenic variants, prevalently in genes encoding the cardiac desmosome (PKP2, DSP, DSC2, DSG2, and JUP) or less frequently in non-desmosomal genes (CTNNA3, PLN, TMEM43, RYR2, SCN5A, CDH2, and DES). Methods: In the present study, we performed molecular autopsy in a boy who died suddenly during physical exertion. In addition to post-mortem examination, a DNA sample was analyzed with next-generation sequencing (NGS). Results: The genetic analysis revealed the presence of pathogenic heterozygous c.314del (p.Pro105Leufs*7) frameshift variant in the PKP2 gene. Cascade screening of family members allowed us to identify 12 mutation carriers and to intervene on subjects at risk, many of whom were athletes. Conclusions: Molecular autopsy can establish cardiogenetic diagnosis and allow appropriate preventative measures in high-risk relatives.
Collapse
Affiliation(s)
- Maria Pia Leone
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Johan Saenen
- Department of Cardiology, University Hospital Antwerp, University Antwerp, Antwerp, Belgium
| | - Sandra Mastroianno
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatic Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo - Istituto Mendel, Rome, Italy
| | - Cesare Amico
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Bioinformatic Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo - Istituto Mendel, Rome, Italy
| | - Domenico Rosario Potenza
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Antonio Petracca
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Di Stolfo
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| |
Collapse
|